U.S. patent number 8,795,970 [Application Number 13/468,323] was granted by the patent office on 2014-08-05 for methods of monitoring conditions by sequence analysis.
This patent grant is currently assigned to Sequenta, Inc.. The grantee listed for this patent is Malek Faham, Thomas Willis. Invention is credited to Malek Faham, Thomas Willis.
United States Patent |
8,795,970 |
Faham , et al. |
August 5, 2014 |
**Please see images for:
( Certificate of Correction ) ** |
Methods of monitoring conditions by sequence analysis
Abstract
There is a need for improved methods for determining the
diagnosis and prognosis of patients with conditions, including
autoimmune disease and cancer. Provided herein are methods for
using DNA sequencing to identify personalized biomarkers in
patients with autoimmune disease and other conditions. Identified
biomarkers can be used to determine the disease state for a subject
with an autoimmune disease or other condition.
Inventors: |
Faham; Malek (Pacifica, CA),
Willis; Thomas (San Francisco, CA) |
Applicant: |
Name |
City |
State |
Country |
Type |
Faham; Malek
Willis; Thomas |
Pacifica
San Francisco |
CA
CA |
US
US |
|
|
Assignee: |
Sequenta, Inc. (South San
Francisco, CA)
|
Family
ID: |
42153463 |
Appl.
No.: |
13/468,323 |
Filed: |
May 10, 2012 |
Prior Publication Data
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|
|
Document
Identifier |
Publication Date |
|
US 20130017957 A1 |
Jan 17, 2013 |
|
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
Issue Date |
|
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12615263 |
Nov 9, 2009 |
8236503 |
|
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61112693 |
Nov 7, 2008 |
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Current U.S.
Class: |
435/6.12;
435/91.2; 435/91.1 |
Current CPC
Class: |
C12Q
1/6869 (20130101); C12Q 1/6881 (20130101); C12Q
1/6883 (20130101); C12Q 1/6886 (20130101); C12N
15/1072 (20130101); C12Q 1/6809 (20130101); C12Q
1/6827 (20130101); Y02A 90/10 (20180101); C12Q
2600/156 (20130101); C12Q 2600/158 (20130101); C12Q
2600/118 (20130101); C12Q 2600/16 (20130101); C12Q
2600/106 (20130101) |
Current International
Class: |
C12Q
1/68 (20060101); C12P 19/34 (20060101) |
Field of
Search: |
;435/6.12,91.1,91.2 |
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|
Primary Examiner: Horlick; Kenneth R.
Assistant Examiner: Tung; Joyce
Attorney, Agent or Firm: Wilson Sonsini Goodrich &
Rosati
Parent Case Text
CROSS REFERENCE
This is a continuation application of U.S. utility application Ser.
No. 12/615,263 filed 9 Nov. 2009, which application claims the
benefit of U.S. provisional application Ser. No. 61/112,693 filed 7
Nov. 2008; both of the foregoing applications are hereby
incorporated by reference in their entireties.
Claims
What is claimed is:
1. A method for monitoring an autoimmune disease, an infections
disease or a cancer of an individual comprising: (a) obtaining a
sample from the individual comprising T-cells and/or B-cells; (b)
amplifying molecules of nucleic acid from said cells of the sample,
the molecules of nucleic acid comprising sequences of
complementarily determining region 3 (CDR3) from T-cell receptor
genes or immunoglobulin genes; (c) spatially isolating individual
molecules of the amplified nucleic acids; (d) sequencing the
spatially isolated individual molecules of the amplified nucleic
acids to provide a full repertoire of CDR3 sequences comprising at
least 1000 sequence reads of at least 30 bp; and (e) monitoring the
autoimmune disease, infectious disease or cancer by determining
levels of one or more CDR3 sequences that correlate with the
disease or cancer.
2. The method of claim 1 wherein CDR3 sequences of said full
repertoire of CDR3 sequences each include a V segment and wherein
said step of amplifying includes amplifying in a polymerase chain
reaction using primers specific for each of the V segments.
3. The method of claim 2 wherein said one or more correlating CDR3
sequences are distinguished among said full repertoire of CDR3
sequences by V, D, and J segments used.
4. The method of claim 2 wherein said sequences of CDR3 are from
said immunoglobulin genes and have a level of somatic mutations and
wherein said one or more correlating CDR3 sequences are
distinguished among said full repertoire of CDR3 sequences by the
level of somatic mutations in each of said one or more correlating
CDR3 sequences.
5. The method of claim 2 wherein said CDR3 sequences each have a
level within said full repertoire of CDR3 sequences and wherein
said one or more correlating CDR3 sequences are distinguished among
said full repertoire of CDR3 sequences by the level of each of said
one or more correlating CDR3 sequences.
6. The method of any one of claims 1 to 5 wherein said sample
comprises at least 1000 B-cells or at least 1000 T-cells.
7. The method of any one of claims 1 to 5 wherein said sample is
blood.
8. The method of any one of claims 1 to 5 wherein said full
repertoire of CDR3 sequences is from T-cell receptor .beta. genes.
Description
SEQUENCE LISTING
The instant application contains a Sequence Listing that was
originally filed via EFS-Web on Feb. 23, 2010 in parent application
Ser. No. 12/615,263. Said ASCII copy, created on Jan. 19, 2010, is
named 37626701.txt, and is 30,869 bytes in size, and is hereby
incorporated by reference in its entirety.
BACKGROUND OF THE INVENTION
The immune system comprises the innate and the adaptive immunity
systems. The innate immune system comprises the cells and
mechanisms utilizing generic methods to recognize foreign
pathogens. Cells involved in innate immunity include neutrophils,
natural killer cells, macrophages, monocytes, basophils,
eosinphils, mast, and dentritic cells. These cells carry out the
act of phagocytosis as well as the release of many chemicals that
kill invading pathogens. In addition, these cells are involved in
innate immunity defense mechanisms including the complement cascade
and inflammation. Finally, some of these cells participate in the
antigen presentation process that plays a role in the adaptive
immunity system.
The adaptive immunity system has evolved to attack specific
features on their targets. The occurrence of one response to a
specific target provides the host with "memory" of it, causing it
to mount a stronger response if it were to appear another time.
Usually any protein or polysaccharide can serve as the target for
some subset of the adaptive immune response cells or their products
that recognize specific epitopes on the target. The adaptive immune
response is divided into two types: the humoral and the
cell-mediated immune response, and B-cells and T-cells play the
specificity roles in these responses, respectively.
Since autoimmune disease involves the recognition of some element
of the adaptive immune system to self targets, aspects of the
adaptive immune system have been examined to aid in diagnosis and
prognosis. Using standard immunological techniques, the humoral
immune system has been investigated by looking for circulating
autoantibodies. Autoantibodies, like antinuclear, anti-dsDNA, and
rheumatoid factor, have been identified for several diseases. These
antibodies may not themselves be pathological, nor is the target
they recognize in the body necessarily the same as that tested for
in vitro; however, measurement of their levels aids in the
diagnosis and in some cases has some prognostic and treatment
implications.
Another methodology to study the adaptive immune system in
autoimmune disease is based on the analysis of the diversity of the
adaptive immune cells. Activation of the adaptive immune cells
leads to their clonal expansion. Evidence of this clonal expansion
is usually achieved by amplification from the blood RNA or DNA of
part of the nucleic acid sequence coding for the antigen
recognition region. For example, PCR primers to amplify sequences
that have a specific V segment of the .beta. chain in T-cell
receptor (analogous to antibody heavy chain) are used to amplify
the J segments or J and D segments connected to the specific V
segment. When a diverse cell population is present it is expected
to amplify fragments with a distribution of slightly different size
amplicons, but clonal expansion causes specific sizes to become
enriched and thus more intense as visualized as bands on a get. In
the technique called spectratyping each of the V segments is
amplified with the J and D segments to assess whether any of these
amplicons shows a clonal expansion.
One problem of the spectratyping approach is that many distinct
sequences can have the same length and hence are indistinguishable.
Therefore only dramatic clonal expansion can be discerned by this
technique. There is need to improve methods of diagnosing and
aiding prognosis of autoimmune disease and autoimmune disease
states as well as other diseases for which the immune system plays
a central role.
While additional specificity in profiling the immune system would
be of great utility in allowing its impact on human health to be
better predicted, still greater utility would be delivered if
methods were developed that would allow the specific T and B cells
involved in disease processes to be identified even if those
particular sequences had never before been observed. The vast
diversity of the immune system provides it with an immense reserve
of potentially useful cells but also presents a challenge to the
researcher trying to use this repertoire for predictive purposes.
Any single sequence targeting an antigen is one of a vast number
that could be involved with and/or correlated to the disease
process in a given individual. Methods that would identify which of
the many cells in a given individual are involved with disease
processes would be of great value to human health.
SUMMARY OF THE INVENTION
In one aspect, a method for determining a profile of recombined DNA
sequences in T-cells and/or B-cells is provided comprising:
obtaining a sample from a subject comprising T-cells and/or
B-cells, spatially isolating individual molecules of genomic DNA
from said cells; sequencing said spatially isolated individual
molecules of genomic DNA, and determining the levels of different
sequences from said sample to generate said profile of recombined
DNA sequences.
In another aspect, a method for determining a profile of recombined
DNA sequences in T-cells and/or B-cells is provided comprising:
obtaining a sample from a subject comprising T-cells and/or
B-cells, spatially isolating individual molecules of genomic DNA
from said cells, amplifying said individual molecules of genomic
DNA, sequencing said amplified DNA, and determining the levels of
different sequences from said sample to generate said profile of
recombined DNA sequences.
In another aspect, a method for determining a profile of recombined
DNA sequences in T-cells and/or B-cells is provided comprising:
obtaining a sample from a subject comprising T-cells and/or
B-cells, amplifying genomic DNA from said cells, spatially
isolating individual molecules of said amplified DNA, sequencing
said spatially isolated individual molecules of amplified DNA; and
determining the levels of different sequences from said sample to
generate said profile of recombined DNA sequences.
In another aspect, a method for determining a profile of recombined
DNA sequences in T-cells and/or B-cells is provided comprising:
obtaining a sample from a subject comprising T-cells and/or
B-cells, amplifying genomic DNA from said cells, spatially
isolating individual molecules of said amplified DNA, re-amplifying
said amplified DNA molecules, sequencing said re-amplified DNA
molecules, and determining the levels of different sequences from
said sample to generate said profile of recombined DNA
sequences.
In another aspect, a method for determining a profile of sequences
of recombined DNA in T-cells and/or B-cells is provided comprising:
obtaining a sample from a subject comprising T-cells and/or
B-cells, reverse transcribing RNA from said cells to form cDNA,
spatially isolating individual molecules of said cDNA, optionally
re-amplifying said spatially isolated individual molecules of cDNA,
sequencing said cDNA and/or re-amplified cDNA; and determining the
levels of different sequences from said sample to generate said
profile of recombined DNA sequences.
In another aspect, a method for determining a profile of recombined
DNA sequences in T-cells and/or B-cells is provided comprising:
obtaining a sample from a subject comprising T-cells and/or
B-cells; spatially isolating individual cells in said sample,
sequencing individual molecules of nucleic from said cells; and
determining the levels of different sequences from said sample to
generate said profile of recombined DNA sequences.
In one embodiment, said amplifying and/or re-amplifying comprises
PCR, multiplex PCR, TMA, NASBA, or LAMP. In another embodiment,
said spatially isolating comprises subcloning said DNA or cDNA in
vectors used to transform bacteria, separating said DNA or cDNA in
two dimensions on a solid support, separating said DNA or cDNA in
three dimensions in a solution with micelles, or separating
molecules using micro-reaction chambers. In another embodiment,
said amplifying and/or re-amplifying is by growth of bacteria
harboring subcloned DNA or cDNA, amplification of DNA or cDNA on a
slide, or amplification of DNA or cDNA on a bead.
In another embodiment, said sequencing comprises dideoxy
sequencing. In another embodiment, said sequencing comprises
sequencing by synthesis using reversibly terminated labeled
nucleotides. In another embodiment, said sequencing comprises
detection of pyrophosphate release on nucleotide incorporation. In
another embodiment, said sequencing comprises allele specific
hybridization to a library of labeled oligonucleotide probes. In
another embodiment, said sequencing comprises sequencing by
synthesis using allele specific hybridization to a library of
labeled oligonucleotide probes followed by ligation of said probes.
In another embodiment, said sequencing comprises real time
monitoring of the incorporation of labeled nucleotides during a
polymerization step.
In another embodiment, said recombined DNA sequences comprise
T-cell receptor genes and/or immunoglobulin genes. In another
embodiment, said sequencing comprises sequencing a subset of the
full clonal sequences of immunoglobulin an/or T-cell receptor
genes.
In another embodiment, said subset of the full clonal sequence
comprises the V-D junction, D-J junction of an immunoglobulin or
T-cell receptor gene, the full variable region of an immunoglobulin
or T-cell receptor gene, the antigen recognition region, or the
complementarity determining region 3 (CDR3). In another embodiment,
said T-cell receptor genes comprise T-cell receptor .beta. genes.
In another embodiment, said immunoglobulin genes comprise
immunoglobulin heavy genes. In another embodiment, said amplifying
or re-amplifying comprises a plurality of primers complementary to
V segments and one primer complementary to a C segment. In another
embodiment, said amplifying or re-amplifying comprises a plurality
of primers complementary to V segments and a plurality of primers
complementary to C segments.
In another embodiment, said plurality of primers complementary to V
segments comprises at least three different primers for each V
segment and the plurality of primers complementary to C segments
comprises at least 1, at least 2, at least 3, at least 4, at least
5, or at least 6 primers.
In another embodiment, said T- or B-cells are subsets of the total
T and B cells. In another embodiment, said subset of T-cells are
CD4+, CD8+ cells, or CD27.sup.high cells. In another embodiment,
said sample comprises at least 100,000, at least 500,000, at least
750,000, of at least 1,000,000 T-cells.
In another embodiment, said sequencing comprises at least 1000
reads per run, at least 10,000 reads per run, at least 100,000
reads per run, or at least 1,000,000 reads per run. In another
embodiment, said sequencing comprises generating about 30 bp, about
40 bp, about 50 bp, about 60 bp, about 70 bp, about 80 bp, about 90
bp, about 100 bp, about 110, or about 120 bp per read.
In another embodiment, said sample is taken when the subject is at
a flare state of an autoimmune disease. In another embodiment, said
sample is taken from a subject having or suspected of having
systemic lupus erythematosus.
In another aspect, a method for determining one or more correlating
clonotypes in a subject is provided comprising: generating one or
more clonotype profiles by nucleic acid sequencing individual,
spatially isolated molecules from at least one sample from the
subject, wherein the at least one sample is related to a first
state of the disease, and determining one or more correlating
clonotypes in the subject based on the one or more clonotype
profiles.
In one embodiment, said at least one sample is from a tissue
affected by the disease. In another embodiment, said determination
of one or more correlating clonotypes comprises comparing clonotype
profiles from at least two samples.
In another embodiment, the first state of the disease is a peak
state of the disease. In another embodiment, said one or more
correlating clonotypes are present in the peak state of the
disease. In another embodiment, said one or more correlating
clonotypes are absent in the peak state of the disease. In another
embodiment, said one or more correlating clonotypes are high in the
peak state of the disease. In another embodiment, said one or more
correlating clonotypes are low in the peak state of the
disease.
In another embodiment, said sample comprises T-cells and/or
B-cells. In another embodiment, said T-cells and/or B-cells
comprise a subset of T-cells and/or B-cells. In another embodiment,
said subset of T-cells and/or B-cells are enriched by interaction
with a marker. In another embodiment, said marker is a cell surface
marker on the subset of T-cells and/or B-cells. In another
embodiment, said subset of T-cells and/or B-cells interact with an
antigen specifically present in the disease.
In another embodiment, the disease is systemic lupus erythematosus
or multiple sclerosis.
In another aspect, a method for developing an algorithm that can
predict one or more correlating clonotypes in any sample from a
subject with a disease is provided comprising: a) generating a
plurality of clonotype profiles from a set of samples, wherein the
samples are relevant to the disease, b) identifying one or more
correlating clonotypes from the set of samples, c) using sequence
parameters and/or functional data from one or more correlating
clonotypes identified in b) to develop the algorithm that can
predict correlating clonotypes in any sample from a subject with
the disease.
In one embodiment, the set of samples are taken from one or more
tissues affected by the disease.
In another embodiment, said identification of one or more
correlating clonotypes comprises comparing clonotype profiles from
at least two samples.
In another embodiment, said functional data include binding ability
of markers on T-cell and/or B-cell surface or interaction with
antigen by a T-cell or B-cell.
In another embodiment, said sequence parameters comprise nucleic
acid sequence and predicted amino acid sequence.
In another embodiment, the samples are from one or more individuals
at a peak stage of the disease. In another embodiment, said one or
more correlating clonotypes are present in the peak state of the
disease. In another embodiment, said one or more correlating
clonotypes are at a high level in the peak state of the disease. In
another embodiment, said one or more correlating clonotypes are at
a low level in the peak state of the disease. In another
embodiment, the one or more correlating clonotypes are absent at
the peak state of the disease. In another embodiment, the disease
is systemic lupus erythematosus or multiple sclerosis.
In another embodiment, a method for discovering one or more
correlating clonotypes for an individual is provided, comprising
inputting a clonotype profile from a sample from the individual
into an algorithm, and using the algorithm to determine one or more
correlating clonotypes for the individual. In one embodiment, the
algorithm is an algorithm that can predict one or more correlating
clonotypes in any sample from a subject with a disease is provided
comprising, said algorithm being developed by: a) generating a
plurality of clonotype profiles from a set of samples, wherein the
samples are relevant to the disease, b) identifying one or more
correlating clonotypes from the set of samples, c) using sequence
parameters and/or functional data from one or more correlating
clonotypes identified in b) to develop an algorithm that can
predict correlating clonotypes in any sample from a subject with
the disease.
In one embodiment, said sample is at taken at a peak state of
disease. In another embodiment, the sample is taken from disease
affected tissue.
In another aspect, a method for generating an algorithm that
calculates a disease activity score is provided comprising:
developing an algorithm that uses a set of factors to combine
levels of correlating clonotypes into a disease activity score,
comparing the disease activity score to clinical data regarding the
disease state, and optimizing the factors in order to maximize the
correlation between clinical data and the disease activity
score.
In one embodiment, method for monitoring the disease state of an
individual is provided comprising: a) determining a clonotype
profile from a sample from the individual, b) inputting the
clonotype profile information from a) into an algorithm that
calculates a disease activity score, wherein is algorithm is
generated by developing an algorithm that uses a set of factors to
combine levels of correlating clonotypes into a disease activity
score, comparing the disease activity score to clinical data
regarding the disease state, and optimizing the factors in order to
maximize the correlation between clinical data and the disease
activity score, and c) using the algorithm that calculates a
disease activity score to generate a score predictive of the
disease state of the individual.
In another embodiment, the method for monitoring the disease state
of an individual further comprises determining one or more
correlating clonotypes in the individual, and inputting information
the one or more correlating clonotypes into the algorithm.
In another embodiment, said determining one or more correlating
clonotypes in the individual comprises a) generating one or more
clonotype profiles by nucleic acid sequencing individual, spatially
isolated molecules from at least one sample from the subject,
wherein the at least one sample is related to a first state of the
disease, and b) determining one or more correlating clonotypes in
the subject based on the one or more clonotype profiles.
In another embodiment, said determining one or more correlating
clonotypes in the individual comprises a) inputting a clonotype
profile from a sample from the individual into an algorithm that
can predict one or more correlating clonotypes, wherein said
algorithm that can predict one or more correlating clonotypes is
developed by i) generating a plurality of clonotype profiles from a
set of samples, wherein the samples are relevant to the disease,
ii) identifying one or more correlating clonotypes from the set of
samples, iii) using sequence parameters and/or functional data from
one or more correlating clonotypes identified in ii) to develop the
algorithm that can predict correlating clonotypes in any sample
from a subject with the disease, and c) using the algorithm that
can predict one or more correlating clonotypes to determine one or
more correlating clonotypes for the individual.
In another embodiment, the disease is systemic lupus erythematosus
or multiple sclerosis.
INCORPORATION BY REFERENCE
All publications, patents, and patent applications mentioned in
this specification are herein incorporated by reference to the same
extent as if each individual publication, patent, or patent
application was specifically and individually indicated to be
incorporated by reference.
BRIEF DESCRIPTION OF THE DRAWINGS
The novel features of the invention are set forth with
particularity in the appended claims. A better understanding of the
features and advantages of the present invention will be obtained
by reference to the following detailed description that sets forth
illustrative embodiments, in which the principles of the invention
are utilized, and the accompanying drawings of which:
FIG. 1 is a flow diagram of an embodiment of a method of the
provided invention for determining clonotype profiles.
FIG. 2 shows a PCR scheme for amplifying TCR.beta. genes. FIG. 2A
discloses SEQ ID NOS 130 and 130-131, respectively, in order of
appearance.
FIG. 3 illustrates a PCR product to be sequenced that was amplified
using the scheme in FIG. 2.
FIGS. 4A and 4B illustrate a PCR scheme for amplifying isotype
sequences. FIG. 4A discloses SEQ ID NOS 132, 132, 132 and 132-134,
respectively, in order of appearance.
FIG. 5 illustrates the reproducibility of multiplexed
amplifications.
FIG. 6 illustrates that multiplexed amplifications have minimal
amplification bias.
FIG. 7 illustrates agarose gel electrophoresis of multiplexed
amplification of IgH sequences.
FIG. 8A shows the log.sub.10 of the frequency of each clonotype in
the two duplicate samples using Accuprime and cDNA corresponding to
500 ng of RNA as input template.
FIG. 8B depicts the log.sub.10 of the frequency of each clonotype
using cDNA corresponding to 500 ng of RNA as input template and
Accuprime (X axis) or High fidelity Taq (Y axis).
FIG. 8C shows the log.sub.10 of the frequency of each clonotype
using cDNA corresponding to 50 ng of RNA as input template and
Accuprime (X axis) or High fidelity Taq (Y axis).
illustrates a flow diagram for determining the algorithm by a
discovery study.
FIG. 9 illustrates one embodiment of a scheme for linking two
sequences to form one amplicon during an amplification reaction.
Information on the presence of these two sequences in the same
sample (e.g., cell) can then be preserved even if they are mixed
with a pool of sequences from other samples.
FIG. 10 illustrates another embodiment of an amplification scheme
for linking two sequences.
FIG. 11 illustrates another embodiment of an amplification scheme
for linking two sequences.
FIGS. 12A and 12B illustrate a scheme for multiplexing the a
reaction linking two sequences by PCR.
FIGS. 13A-13D illustrate a scheme for linking three sequences
together.
FIG. 14 illustrates a flow diagram for discovering correlating
clonotypes using a calibration test.
FIG. 15 illustrates a flow diagram for discovering correlating
clonotypes using a population study.
FIG. 16 illustrates a flow diagram for discovering correlating
clonotypes using a population study and a calibration test.
FIG. 17 illustrates algorithms that can predict correlating
clonotypes in a sample.
FIG. 18 illustrates a flow diagram for generating a monitoring
algorithm for calculating Immune Load.
FIG. 19 illustrates a flow diagram for performing a monitoring test
without a calibration test.
FIG. 20 illustrates a flow diagram for performing a monitoring test
using a calibration test.
DETAILED DESCRIPTION OF THE INVENTION
Overview
In general, the provided invention includes methods for applying
nucleic acid sequencing techniques to the task of monitoring the
repertoire of adaptive immunity cells for profiling the immune
system. The profiles of the immune system generated can be used for
diagnosis of diseases and disorders, and for diagnosis of states of
diseases and disorders. The methods of immune profiling of the
provided invention can be used in monitoring diseases and disorders
and assessing treatment of diseases and disorders. These diseases
and disorders that the methods of the provided invention can be
applied to include autoimmune disease, including systemic lupus
erythematosus (SLE), multiple sclerosis (MS), rheumatoid arthritis
(RA), and ankylosing spondylitis. The methods of the provided
invention can be applied to the diagnosis, monitoring, and
treatment of transplant rejection and immune aging. Furthermore,
the methods of immune profiling of the provided invention can be
used for diagnosing, monitoring, and treating other diseases
related to the immune system, including cancer and infectious
disease.
Sequencing individual amplified molecules can distinguish different
sequences and hence has the sensitivity to detect quantitative
changes in clonal expansion. In general, in one embodiment of the
provided invention, a method for determining a profile of
recombined DNA sequences in T-cells and/or B-cells is provided. The
method can comprise steps including isolating samples from a
subject, one or more rounds of nucleic acid amplification,
spatially isolating individual nucleic acids, and sequencing
nucleic acids. The nucleic acids can be DNA or RNA. The recombined
DNA sequences in T-cells and/or B-cells can be termed
clonotypes.
In one aspect, a method for determining one or more correlating
clonotypes in a subject, or individual is provided. In another
aspect, a method for developing an algorithm that can predict one
or more correlating clonotypes in any sample from a subject with a
disease is provided. In another aspect, a method for discovering
one or more correlating clonotypes for an individual using an
algorithm that can predict one or more correlating clonotypes in
any sample from a subject is provided. In another aspect, a method
for generating an algorithm that calculates a disease activity
score is provided. In another aspect, a method for monitoring the
disease state of an individual is provided.
1. Methods of Determining Clonotype Profiles
A. Overview
The methods of the provided invention can be used to generate
profiles of recombined DNA sequences, or clonotypes, in sample from
a subject.
In one embodiment, a method for determining a profile of recombined
DNA sequences in T-cells and/or B-cells is provided including
obtaining a sample from a subject comprising T-cells and/or
B-cells, isolating individual molecules of genomic DNA from said
cells, sequencing the isolated individual molecules of genomic DNA,
and determining the levels of different sequences from the sample
to generate said profile of recombined DNA sequences.
In another embodiment, a method for determining a profile of
recombined DNA sequences in T-cells and/or B-cells is provided
including obtaining a sample from a subject comprising T-cells
and/or B-cells, isolating individual molecules of genomic DNA from
the cells, amplifying the individual molecules of genomic DNA,
sequencing the amplified DNA, and determining the levels of
different sequences from the sample to generate said profile of
recombined DNA sequences.
In another embodiment, a method for determining a profile of
recombined DNA sequences in T-cells and/or B-cells is provided
including obtaining a sample from a subject comprising T-cells
and/or B-cells, amplifying genomic DNA from the cells, isolating
individual molecules of the amplified DNA, sequencing the isolated
individual molecules of amplified DNA, and determining the levels
of different sequences from the sample to generate the profile of
recombined DNA sequences.
In another embodiment, a method for determining a profile of
recombined DNA sequences in T-cells and/or B-cells is provided
including obtaining a sample from a subject including T-cells
and/or B-cells, amplifying genomic DNA from the cells, isolating
individual molecules of the amplified DNA, re-amplifying the
amplified DNA molecules, sequencing the re-amplified DNA molecules,
and determining the levels of different sequences from the sample
to generate the profile of recombined DNA sequences.
In another embodiment, a method for determining a profile of
sequences of recombined DNA in T-cells and/or B-cells is provided
including obtaining a sample from a subject comprising T-cells
and/or B-cells, isolating RNA from said sample, reverse
transcribing the RNA from said cells to form cDNA, isolating
individual molecules of said cDNA, optionally re-amplifying said
cDNA, sequencing said isolated individual molecules of said cDNA or
re-amplified DNA, and determining the levels of different sequences
from said sample to generate said profile of recombined DNA
sequences.
In another embodiment, a method for determining a profile of
sequences of recombined DNA in T-cells and/or B-cells is provided
including obtaining a sample from a subject including T-cells
and/or B-cells, isolating individual molecules of RNA from said
sample, sequencing the individual molecules of RNA, and determining
the levels of different sequences from said sample to generate the
profile of recombined DNA sequences.
B. Subjects and Samples
1. Subjects
The methods of the provided invention can use samples from subjects
or individuals (e.g., patients). The subject can be a patient, for
example, a patient with an autoimmune disease. The subject can be a
patient with an infectious disease or cancer. The subject can be a
mammal, for example, a human. The subject can be male or female.
The subject can be an infant, a child, or an adult.
2. Samples
Samples used in the methods of the provided invention can include,
for example, a bodily fluid from a subject, including amniotic
fluid surrounding a fetus, aqueous humor, bile, blood and blood
plasma, cerumen (earwax), Cowper's fluid or pre-ejaculatory fluid,
chyle, chyme, female ejaculate, interstitial fluid, lymph, menses,
breast milk, mucus (including snot and phlegm), pleural fluid, pus,
saliva, sebum (skin oil), semen, serum, sweat, tears, urine,
vaginal lubrication, vomit, water, feces, internal body fluids,
including cerebrospinal fluid surrounding the brain and the spinal
cord, synovial fluid surrounding bone joints, intracellular fluid
is the fluid inside cells, and vitreous humour the fluids in the
eyeball. In one embodiment, the sample is a blood sample. The blood
sample can be about 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9,
1.0, 1.5, 2.0, 2.5, 3.0, 3.5, 4.0, 4.5, or 5.0 mL. The sample can
be Cerebral Spinal Fluid (CSF) when the subject has multiple
sclerosis, synovial fluid when the subject has rheumatoid
arthritis, and skin (or other organ) biopsy when the subject has
systemic lupus. In one embodiment, the clonotpe can be identified
from the available body fluid/tissue most likely to reflect
pathology followed by later monitoring the levels of the clonotypes
form a different body fluid, for example, blood.
Samples can be analyzed at a time when the disease is inactive.
The sample can be obtained by a health care provider, for example,
a physician, physician assistant, nurse, veterinarian,
dermatologist, rheumatologist, dentist, paramedic, or surgeon. The
sample can be obtained by a research technician. More than one
sample from a subject can be obtained.
The sample can be a biopsy, e.g., a skin biopsy. The biopsy can be
from, for example, brain, liver, lung, heart, colon, kidney, or
bone marrow. Any biopsy technique used by those skilled in the art
can be used for isolating a sample from a subject. For example, a
biopsy can be an open biopsy, in which general anesthesia is used.
The biopsy can be a closed biopsy, in which a smaller cut is made
than in an open biopsy. The biopsy can be a core or incisional
biopsy, in which part of the tissue is removed. The biopsy can be
an excisional biopsy, in which attempts to remove an entire lesion
are made. The biopsy can be a fine needle aspiration biopsy, in
which a sample of tissue or fluid is removed with a needle.
The sample can include immune cells. The immune cells can include
T-cells and/or B-cells. T-cells (T lymphocytes) include, for
example, cells that express T cell receptors. T-cells include
Helper T cells (effector T cells or Th cells), cytotoxic T cells
(CTLs), memory T cells, and regulatory T cells. The sample can
include a single cell in some applications (e.g., a calibration
test to define relevant T cells) or more generally at least 1,000,
at least 10,000, at least 100,000, at least 250,000, at least
500,000, at least 750,000, or at least 1,000,000 T-cells.
B-cells include, for example, plasma B cells, memory B cells, B1
cells, B2 cells, marginal-zone B cells, and follicular B cells.
B-cells can express immunoglobulins (antibodies, B cell receptor).
The sample can include a single cell in some applications (e.g., a
calibration test to define relevant B cells) or more generally at
least 1,000, at least 10,000, at least 100,000, at least 250,000,
at least 500,000, at least 750,000, or at least 1,000,000
B-cells.
The sample can include nucleic acid, for example, DNA (e.g.,
genomic DNA or mitochondrial DNA) or RNA (e.g., messenger RNA or
microRNA). The nucleic acid can be cell-free DNA or RNA. In the
methods of the provided invention, the amount of RNA or DNA from a
subject that can be analyzed includes, for example as low as a
single cell in some applications (e.g., a calibration test) and as
many as 10 millions of cells or more translating to a range of DNA
of 6 pg-60 ug, and RNA of approximately 1 pg-10 ug.
C. Means for Isolating, Amplifying and Re-Amplifying Nucleic
Acid
1. Characteristics of TCR and BCR Genes
Since the identifying recombinations are present in the DNA of each
individual adaptive immunity cell as well as their associated RNA
transcripts, either RNA or DNA can be sequenced in the methods of
the provided invention. A recombined sequence from a T-cell or
B-cell can also be referred to as a clonotype. The DNA or RNA can
correspond to sequences from T-cell receptor (TCR) genes or
immunoglobulin (Ig) genes that encode antibodies. For example, the
DNA and RNA can correspond to sequences encoding .alpha., .beta.,
.gamma., or .delta. chains of a TCR. In a majority of T-cells, the
TCR is a heterodimer consisting of an .alpha.-chain and
.beta.-chain. The TCR.alpha. chain is generated by VJ
recombination, and the .beta. chain receptor is generated by V(D)J
recombination. For the TCR.beta. chain, in humans there are 48 V
segments, 2 D segments, and 13 J segments. Several bases may be
deleted and others added (called N and P nucleotides) at each of
the two junctions. In a minority of T-cells, the TCRs consist of
.gamma. and .delta. delta chains. The TCR .gamma. chain is
generated by VJ recombination, and the TCR .delta. chain is
generated by V(D)J recombination (Kenneth Murphy, Paul Travers, and
Mark Walport, Janeway's Immunology 7th edition, Garland Science,
2007, which is herein incorporated by reference in its
entirety.
The DNA and RNA analyzed in the methods of the provided invention
can correspond to sequences encoding heavy chain immunoglobulins
(IgH) with constant regions (.alpha., .delta., .epsilon., .gamma.,
or .mu.) or light chain immunoglobulins (IgK or IgL) with constant
regions .lamda. or .kappa.. Each antibody has two identical light
chains and two identical heavy chains. Each chain is composed of a
constant (C) and a variable region. For the heavy chain, the
variable region is composed of a variable (V), diversity (D), and
joining (J) segments. Several distinct sequences coding for each
type of these segments are present in the genome. A specific VDJ
recombination event occurs during the development of a B-cell,
marking that cell to generate a specific heavy chain. Diversity in
the light chain is generated in a similar fashion except that there
is no D region so there is only VJ recombination. Somatic mutation
often occurs close to the site of the recombination, causing the
addition or deletion of several nucleotides, further increasing the
diversity of heavy and light chains generated by B-cells. The
possible diversity of the antibodies generated by a B-cell is then
the product of the different heavy and light chains. The variable
regions of the heavy and light chains contribute to form the
antigen recognition (or binding) region or site. Added to this
diversity is a process of somatic hypermutation which can occur
after a specific response is mounted against some epitope. In this
process mutations occur in those B-cells that are able to recognize
the specific epitope leading to greater diversity in antibodies
that may be able to bind the specific epitope more strongly. All
these factors contribute to great diversity of antibodies generated
by the B-cells. Many billions and maybe more than a trillion
distinct antibodies may be generated. The basic premise for
generating T-cell diversity is similar to that for generating
antibodies by B-cells. An element of T-cell and B-cell activation
is their binding to foreign epitopes. The activation of a specific
cell leads to the production of more of the same type of cells
leading to a clonal expansion.
Complementarity determining regions (CDR), or hypervariable
regions, are sequences in the variable domains of antigen receptors
(e.g., T cell receptor and immunoglobulin) that can complement an
antigen. The chain of each antigen receptor contains three CDRs
(CDR1, CDR2, and CDR3). The two polypeptides making T cells
(.alpha. and .beta.) and immunoglobulin (IgH and IgK or IgL)
contribute to the formation of the three CDRs.
The part of CDR1 and CDR2 that is coded for by TCR.beta. lies
within one of 47 functional V segments. Most of the diversity of
CDRs is found in CDR3, with the diversity being generated by
somatic recombination events during the development of T
lymphocytes.
A great diversity of BCR is present inter and intra-individuals.
The BCR is composed of two genes IgH and IgK (or IgL) coding for
antibody heavy and light chains. Three Complementarity Determining
Region (CDR) sequences that bind antigens and MHC molecules have
the most diversity in IgH and IgK (or IgL). The part of CDR1 and
CDR2 coded for by IgH lies within one of 44 functional V segments.
Most of the diversity in naive B cells emerges in the generation of
CDR3 through somatic recombination events during the development of
B lymphocytes. The recombination can generate a molecule with one
of each of the V, D, and J segments. In humans, there are 44 V, 27
D, and 6 J segments; thus, there is a theoretical possibility of
more than 7,000 combinations. In a small fraction of BCRs
(.about.5%) two D segments are found. Furthermore, several bases
may be deleted and others added (called N and P nucleotides) at
each of the two junctions generating a great degree of diversity.
After B cell activation a process of affinity maturation through
somatic hypermutation occurs. In this process progeny cells of the
activated B cells accumulate distinct somatic mutations throughout
the gene with higher mutation concentration in the CDR regions
leading to generating antibodies with higher affinity to the
antigens. Therefore multiple primers can be utilized to amplify
sequences after somatic hypermutation. In addition to somatic
hypermutation activated B cells undergo the process of isotype
switching. Antibodies with the same variable segments can have
different forms (isotypes) depending on the constant segment.
Whereas all naive B cells express IgM (or IgD), activated B cells
mostly express IgG but also IgM, IgA and IgE. This expression
switching from IgM (and/or IgD) to IgG, IgA, or IgE occurs through
a recombination event causing one cell to specialize in producing a
specific isotype. There is one segment for each IgM, IgD, and IgE,
two segments for IgA, and four segments for IgG.
2. Amplification Reactions
Polymerase chain reaction (PCR) can be used to amplify the relevant
regions from a collection of cells. Transcription Mediated
Amplification (TMA) can be used to produce RNA amplicons from a
target nucleic acid. The nucleic acid from each cell can be
analyzed separately, as each cell will carry its own unique
signature.
TCR.beta. or immunoglobulin sequences can be amplified from nucleic
acid in a multiplex reaction using at least one primer that anneals
to the C region and one or more primers that can anneal to one or
more V segments (FIG. 2 and FIG. 4). The number of primers that
anneal to V segments in a multiplex reaction can be, for example,
at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,
18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34,
35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51,
52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68,
69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, or 80. The number of
primers that anneal to V segments in a multiplex reaction can be,
for example, 10-60, 20-50, 30-50, 40-50, 20-40, 30-40, or 35-40.
The primers can anneal to different V segments. For IgH genes,
because of the possibility of somatic mutations in the V segments,
multiple primers that anneal to each V segment can be used; for
example, 1, 2, 3, 4, or 5 primers per V segment. The number of
primers that anneal to C segments in a multiplex reaction can
include, for example, at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11,
12, 13, 14, or 15. The number of primers that anneal to C segments
in a multiplex reaction can be 1-10, 2-9, 3-8, 4-7, 3-8, or 3-6.
Amplification of TCR or immunoglobulin genes can occur as described
in Example 3 and/or Example 4.
The region to be amplified can include the full clonal sequence or
a subset of the clonal sequence, including the V-D junction, D-J
junction of an immunoglobulin or T-cell receptor gene, the full
variable region of an immunoglobulin or T-cell receptor gene, the
antigen recognition region, or a CDR, e.g., complementarity
determining region 3 (CDR3).
The TCR or immunoglobulin sequence can amplified using a primary
and a secondary amplification step. Each of the different
amplification steps can comprise different primers. The different
primers can introduce sequence not original present in the immune
gene sequence. For example, the amplification procedure can add one
or more tags to the 5' and/or 3' end of amplified TCR or
immunoglobulin sequence (FIG. 3). The tag can be sequence that
facilitates subsequent sequencing of the amplified DNA. The tag can
be sequence that facilitates binding the amplified sequence to a
solid support.
Other methods for amplification may not employ any primers in the V
region. Instead, a specific primer can be used from the C segment
and a generic primer can be put in the other side (5'). The generic
primer can be appended in the cDNA synthesis through different
methods including the well described methods of strand switching.
Similarly, the generic primer can be appended after cDNA making
through different methods including ligation.
Other means of amplifying nucleic acid that can be used in the
methods of the provided invention include, for example, reverse
transcription-PCR, real-time PCR, quantitative real-time PCR,
digital PCR (dPCR), digital emulsion PCR (dePCR), clonal PCR,
amplified fragment length polymorphism PCR (AFLP PCR), allele
specific PCR, assembly PCR, asymmetric PCR (in which a great excess
of primers for a chosen strand is used), colony PCR,
helicase-dependent amplification (HDA), Hot Start PCR, inverse PCR
(IPCR), in situ PCR, long PCR (extension of DNA greater than about
5 kilobases), multiplex PCR, nested PCR (uses more than one pair of
primers), single-cell PCR, touchdown PCR, loop-mediated isothermal
PCR (LAMP), and nucleic acid sequence based amplification (NASBA).
Other amplification schemes include: Ligase Chain Reaction, Branch
DNA Amplification, Rolling Circle Amplification, Circle to Circle
Amplification, SPIA amplification, Target Amplification by Capture
and Ligation (TACL) amplification, and RACE amplification.
The information in RNA in a sample can be converted to cDNA by
using reverse transcription. PolyA primers, random primers, and/or
gene specific primers can be used in reverse transcription
reactions.
After amplification of DNA from the genome (or amplification of
nucleic acid in the form of cDNA by reverse transcribing RNA), the
individual nucleic acid molecules can be isolated, optionally
re-amplified, and then sequenced individually.
Polymerases that can be used for amplification in the methods of
the provided invention include, for example, Taq polymerase,
AccuPrime polymerase, or Pfu. The choice of polymerase to use can
be based on whether fidelity or efficiency is preferred.
In one embodiment, individual cells in a sample are isolated. Two
or more sequences from each isolated cell can be linked together.
For example, sequences from TCR.alpha. and TCR.beta. genes or IgH
and IgK genes from an individual cell can be linked, for example by
an amplification scheme (FIGS. 9-13) or a ligation scheme. The
linked TCR.alpha. and TCR.beta. or IgH and IgK sequences for
isolated cells can optionally be reamplified. The linked
amplification products can be optionally repooled after
amplification.
3. Means of Isolating Individual Nucleic Acids
Methods for isolation of nucleic acids from a pool include
subcloning nucleic acid into DNA vectors and transforming bacteria
(bacterial cloning), spatial separation of the molecules in two
dimensions on a solid substrate (e.g., glass slide), spatial
separation of the molecules in three dimensions in a solution
within micelles (such as can be achieved using oil emulsions with
or without immobilizing the molecules on a solid surface such as
beads), or using microreaction chambers in, for example,
microfluidic or nano-fluidic chips. Dilution can be used to ensure
that on average a single molecule is present in a given volume,
spatial region, bead, or reaction chamber.
Real time PCR, picogreen staining, nanofluidic electrophoresis
(e.g. LabChip) or UV absorption measurements can be used in an
initial step to judge the functional amount of amplifiable
material.
Methods for re-amplification of nucleic acids include bacterial
growth of isolated colonies transformed with nucleic acid,
amplification on a slide (e.g., PCR colonies (polonies)), and
amplification on a bead. The same method can be use to amplify and
re-amplify the nucleic acid or a different method can be used to
amplify and reamplify the nucleic acid.
In certain embodiments the subcloning steps include a step in which
a common primer is attached to the DNA or RNA through an
amplification or ligation step. This primer is then used to amplify
the clones and as a recognition sequence for hybridization of a
primer for sequencing (FIG. 2).
In other embodiments, nucleic acids are analyzed from a subset of
cells. A method to separate cells, for example by using a cell
surface marker, can be employed. For example, cells can be isolated
by cell sorting flow-cytometry, flow-sorting, fluorescent activated
cell sorting (FACS), bead based separation such as magnetic cell
sorting (MACS; e.g., using antibody coated magnetic particles),
size-based separation (e.g., a sieve, an array of obstacles, or a
filter), sorting in a microfluidics device, antibody-based
separation, sedimentation, affinity adsorption, affinity
extraction, or density gradient centrifugation. Cells can be
purified by laser capture microdissection. Sorting can be based on
cell size, morphology, or intracellular or extracellular markers.
Methods for isolating or sorting tumor cells are described, for
example, in Nagrath S. et al. (2007) Nature 450:1235-1239; U.S.
Pat. Nos. 6,008,002, 7,232,653, and 7,332,288; PCT Publication No.
WO2008157220A1; and US Patent Application Nos. US20080138805A1 and
US20090186065; and Rosenberg R. et al. (2002) Cytometry 49:150-158,
each of which is herein incorporated by reference in their
entireties.
The subset of cells can be a subset of T-cells and/or B-cells. The
subset of T cells can be CD4+, CD8+, or CD27.sup.high cells.
Fluorescence-activated cell sorting (FACS) uses light scattering
and fluorescent characteristics to sort cells. A fluorescent
property can be imparted on a cell using, e.g., nucleic acid probes
or antibodies conjugated to a fluorescent dye. A cell suspension
can form a stream of flowing liquid. The stream of cells forms
drops that contain approximately one cell per drop. Before the
stream forms drops, a fluorescent characteristic of each cell is
measured. A charge is placed on an electrical charging ring prior
to fluorescence intensity measurement and the opposite charge is
carried on the drop as it breaks from the stream. The charged drops
pass through two high voltage deflection plates that divert drops
into different containers based upon their charge. The charge can
be directly applied to the stream and the drop breaking off retains
the charge of the same sign as the stream. The stream is then
returned to neutral after the drop breaks off.
Direct or indirect immunofluorescence can be used in FACS. In
direct immunofluorescence, an antibody is directly conjugated to a
fluorescent dye. In indirect immunofluorescence, the primary
antibody is not labeled, and a secondary antibody is conjugated to
a fluorescent dye.
In one embodiment, individual cells from a sample can be isolated.
Sequence information from two more genes in a cell can be linked
together. For example, a sample can be from a patient with an
autoimmune disease, and sequence information from TCR.alpha. and
TCR.beta. genes from spatially isolated cells from the sample can
be physically linked by, for example, an amplification scheme or a
ligation scheme. The linked TCR.alpha. and TCR.beta. sequences can
optionally be amplified and/or pooled with linked sequences from
other cells. The linked sequences can alternatively be for IgH and
IgK or for IgH and IgL
C. Sequencing Techniques
Any technique for sequencing nucleic acid known to those skilled in
the art can be used in the methods of the provided invention. DNA
sequencing techniques include classic dideoxy sequencing reactions
(Sanger method) using labeled terminators or primers and gel
separation in slab or capillary, sequencing by synthesis using
reversibly terminated labeled nucleotides, pyrosequencing, 454
sequencing, allele specific hybridization to a library of labeled
oligonucleotide probes, sequencing by synthesis using allele
specific hybridization to a library of labeled clones that is
followed by ligation, real time monitoring of the incorporation of
labeled nucleotides during a polymerization step, polony
sequencing, and SOLiD sequencing. Sequencing of the separated
molecules has more recently been demonstrated by sequential or
single extension reactions using polymerases or ligases as well as
by single or sequential differential hybridizations with libraries
of probes. These reactions have been performed on many clonal
sequences in parallel including demonstrations in current
commercial applications of over 100 million sequences in parallel.
These sequencing approaches can thus be used to study the
repertoire of T-cell receptor (TCR) and/or B-cell receptor
(BCR).
The sequencing technique used in the methods of the provided
invention can generate least 1000 reads per run, at least 10,000
reads per run, at least 100,000 reads per run, at least 500,000
reads per run, or at least 1,000,000 reads per run. The sequencing
technique used in the methods of the provided invention can
generate about 30 bp, about 40 bp, about 50 bp, about 60 bp, about
70 bp, about 80 bp, about 90 bp, about 100 bp, about 110, about 120
bp per read, about 150 bp, about 200 bp, about 250 bp, about 300
bp, about 350 bp, about 400 bp, about 450 bp, about 500 bp, about
550 bp, or about 600 bp per read.
The sequencing technique used in the methods of the provided
invention can generate at least 30, 40, 50, 60, 70, 80, 90, 100,
110, 120, 150, 200, 250, 300, 350, 400, 450, 500, 550, or 600 bp
per read.
1. True Single Molecule Sequencing
A sequencing technique that can be used in the methods of the
provided invention includes, for example, Helicos True Single
Molecule Sequencing (tSMS) (Harris T. D. et al. (2008) Science
320:106-109). In the tSMS technique, a DNA sample is cleaved into
strands of approximately 100 to 200 nucleotides, and a polyA
sequence is added to the 3' end of each DNA strand. Each strand is
labeled by the addition of a fluorescently labeled adenosine
nucleotide. The DNA strands are then hybridized to a flow cell,
which contains millions of oligo-T capture sites that are
immobilized to the flow cell surface. The templates can be at a
density of about 100 million templates/cm.sup.2. The flow cell is
then loaded into an instrument, e.g., HeliScope.TM. sequencer, and
a laser illuminates the surface of the flow cell, revealing the
position of each template. A CCD camera can map the position of the
templates on the flow cell surface. The template fluorescent label
is then cleaved and washed away. The sequencing reaction begins by
introducing a DNA polymerase and a fluorescently labeled
nucleotide. The oligo-T nucleic acid serves as a primer. The
polymerase incorporates the labeled nucleotides to the primer in a
template directed manner. The polymerase and unincorporated
nucleotides are removed. The templates that have directed
incorporation of the fluorescently labeled nucleotide are detected
by imaging the flow cell surface. After imaging, a cleavage step
removes the fluorescent label, and the process is repeated with
other fluorescently labeled nucleotides until the desired read
length is achieved. Sequence information is collected with each
nucleotide addition step.
2. 454 Sequencing
Another example of a DNA sequencing technique that can be used in
the methods of the provided invention is 454 sequencing (Roche)
(Margulies, M et al. 2005, Nature, 437, 376-380). 454 sequencing
involves two steps. In the first step, DNA is sheared into
fragments of approximately 300-800 base pairs, and the fragments
are blunt ended. Oligonucleotide adaptors are then ligated to the
ends of the fragments. The adaptors serve as primers for
amplification and sequencing of the fragments. The fragments can be
attached to DNA capture beads, e.g., streptavidin-coated beads
using, e.g., Adaptor B, which contains 5'-biotin tag. The fragments
attached to the beads are PCR amplified within droplets of an
oil-water emulsion. The result is multiple copies of clonally
amplified DNA fragments on each bead. In the second step, the beads
are captured in wells (pico-liter sized). Pyrosequencing is
performed on each DNA fragment in parallel. Addition of one or more
nucleotides generates a light signal that is recorded by a CCD
camera in a sequencing instrument. The signal strength is
proportional to the number of nucleotides incorporated.
Pyrosequencing makes use of pyrophosphate (PPi) which is released
upon nucleotide addition. PPi is converted to ATP by ATP
sulfurylase in the presence of adenosine 5' phosphosulfate.
Luciferase uses ATP to convert luciferin to oxyluciferin, and this
reaction generates light that is detected and analyzed.
3. SOLiD Sequencing
Another example of a DNA sequencing technique that can be used in
the methods of the provided invention is SOLiD technology (Applied
Biosystems). In SOLiD sequencing, genomic DNA is sheared into
fragments, and adaptors are attached to the 5' and 3' ends of the
fragments to generate a fragment library. Alternatively, internal
adaptors can be introduced by ligating adaptors to the 5' and 3'
ends of the fragments, circularizing the fragments, digesting the
circularized fragment to generate an internal adaptor, and
attaching adaptors to the 5' and 3' ends of the resulting fragments
to generate a mate-paired library. Next, clonal bead populations
are prepared in microreactors containing beads, primers, template,
and PCR components. Following PCR, the templates are denatured and
beads are enriched to separate the beads with extended templates.
Templates on the selected beads are subjected to a 3' modification
that permits bonding to a glass slide.
The sequence can be determined by sequential hybridization and
ligation of partially random oligonucleotides with a central
determined base (or pair of bases) that is identified by a specific
fluorophore. After a color is recorded, the ligated oligonucleotide
is cleaved and removed and the process is then repeated.
4. SOLEXA Sequencing
Another example of a sequencing technology that can be used in the
methods of the provided invention is SOLEXA sequencing (Illumina).
SOLEXA sequencing is based on the amplification of DNA on a solid
surface using fold-back PCR and anchored primers. Genomic DNA is
fragmented, and adapters are added to the 5' and 3' ends of the
fragments. DNA fragments that are attached to the surface of flow
cell channels are extended and bridge amplified. The fragments
become double stranded, and the double stranded molecules are
denatured. Multiple cycles of the solid-phase amplification
followed by denaturation can create several million clusters of
approximately 1,000 copies of single-stranded DNA molecules of the
same template in each channel of the flow cell. Primers, DNA
polymerase and four fluorophore-labeled, reversibly terminating
nucleotides are used to perform sequential sequencing. After
nucleotide incorporation, a laser is used to excite the
fluorophores, and an image is captured and the identity of the
first base is recorded. The 3' terminators and fluorophores from
each incorporated base are removed and the incorporation, detection
and identification steps are repeated.
5. SMRT Sequencing
Another example of a sequencing technology that can be used in the
methods of the provided invention includes the single molecule,
real-time (SMRT.TM.) technology of Pacific Biosciences. In SMRT,
each of the four DNA bases is attached to one of four different
fluorescent dyes. These dyes are phospholinked. A single DNA
polymerase is immobilized with a single molecule of template single
stranded DNA at the bottom of a zero-mode waveguide (ZMW). A ZMW is
a confinement structure which enables observation of incorporation
of a single nucleotide by DNA polymerase against the background of
fluorescent nucleotides that rapidly diffuse in an out of the ZMW
(in microseconds). It takes several milliseconds to incorporate a
nucleotide into a growing strand. During this time, the fluorescent
label is excited and produces a fluorescent signal, and the
fluorescent tag is cleaved off. Detection of the corresponding
fluorescence of the dye indicates which base was incorporated. The
process is repeated.
6. Nanopore Sequencing
Another example of a sequencing technique that can be used is the
methods of the provided invention is nanopore sequencing (Soni G V
and Meller A. (2007) Clin Chem 53: 1996-2001). A nanopore is a
small hole, of the order of 1 nanometer in diameter. Immersion of a
nanopore in a conducting fluid and application of a potential
across it results in a slight electrical current due to conduction
of ions through the nanopore. The amount of current which flows is
sensitive to the size of the nanopore. As a DNA molecule passes
through a nanopore, each nucleotide on the DNA molecule obstructs
the nanopore to a different degree. Thus, the change in the current
passing through the nanopore as the DNA molecule passes through the
nanopore represents a reading of the DNA sequence.
7. Chemical-Sensitive Field Effect Transistor Array Sequencing
Another example of a sequencing technique that can be used in the
methods of the provided invention involves using a
chemical-sensitive field effect transistor (chemFET) array to
sequence DNA (for example, as described in US Patent Application
Publication No. 20090026082). In one example of the technique, DNA
molecules can be placed into reaction chambers, and the template
molecules can be hybridized to a sequencing primer bound to a
polymerase. Incorporation of one or more triphosphates into a new
nucleic acid strand at the 3' end of the sequencing primer can be
detected by a change in current by a chemFET. An array can have
multiple chemFET sensors. In another example, single nucleic acids
can be attached to beads, and the nucleic acids can be amplified on
the bead, and the individual beads can be transferred to individual
reaction chambers on a chemFET array, with each chamber having a
chemFET sensor, and the nucleic acids can be sequenced.
8. Sequencing with an Electron Microscope
Another example of a sequencing technique that can be used in the
methods of the provided invention involves using a electron
microscope (Moudrianakis E. N. and Beer M. Proc Natl Acad Sci USA.
1965 March; 53:564-71). In one example of the technique, individual
DNA molecules are labeled using metallic labels that are
distinguishable using an electron microscope. These molecules are
then stretched on a flat surface and imaged using an electron
microscope to measure sequences.
Any one of the sequencing techniques described herein can be used
in the methods of the provided invention.
D. Methods for Sequencing the TCR and BCR Repertoire
Sequences can be read that originate from a single molecule or that
originate from amplifications from a single molecule. Millions of
independent amplifications of single molecules can be performed in
parallel either on a solid surface or in tiny compartments in
water/oil emulsion. The DNA sample to be sequenced can be diluted
and/or dispersed sufficiently to obtain one molecule in each
compartment. This dilution can be followed by DNA amplification to
generate copies of the original DNA sequences and creating
"clusters" of molecules all having the same sequence. These
clusters can then be sequenced. Many millions of reads can be
generated in one run. Sequence can be generated starting at the 5'
end of a given strand of an amplified sequence and/or sequence can
be generated from starting from the 5' end of the complementary
sequence. In a preferred embodiment, sequence from strands is
generated, i.e. paired end reads.
The prevalence of a particular sequence in the original DNA
sequence can then be measured by counting how many clusters carry
that sequence. More prevalent sequences in the original sample lead
to more compartments and more clusters containing the specific
sequences.
Methods can be used in the amplification schemes to ensure that the
frequency of the DNA sequences measured matches the frequency of
the DNA sequence in the original sample. The methods can include
ensuring that PCR primer concentration are high enough to drive
each hybridization reaction to saturation in each cycle, adjusting
individual primer concentrations to minimize the differential
amplification of different sequences, etc.
Algorithms can be used to determine which sequences generated by
the sequencer originate from the DNA sequence. Individually
measured sequences (reads) may be offset relative to each other,
contain errors introduced by amplification and/or by sequencing. An
algorithm can be used to combine reads together to more accurately
determine the frequency of a DNA sequence in the starting
material.
A million sequencing reads or more for IgH and/or TCR.beta.
originally amplified from a blood sample comprising DNA or RNA can
be obtained. The number of reads for a specific IgH or TCR.beta.
sequence relate to the frequency of the specific clonotype in the
blood sample. Therefore, the quantity of each of the clonotypes can
be determined. If the pathogenic clonotypes for a particular
patient are known, their level can be determined accurately through
this sequencing approach.
In certain embodiments of the provided invention, a collection of
DNA molecules including a representation of the genomic DNA or
reverse transcribed RNA from the TCR and BCR regions of immune
cells from one or more subjects is extracted and optionally
amplified in such a way that each molecule can be sequenced using
one or more of the sequencing techniques described above in order
to be able to detect the presence and frequency of sequences in a
subject.
Different regions of immunoglobulin or T cell receptor genes can be
sequenced. In some embodiments, the full sequence of the variable
regions can be sequenced to identify and quantify a clonotype.
A unique subset of the full clonal sequences can be sequenced. In
some embodiments, nucleotides comprising the VD and the DJ
junctions are sequenced to uniquely identify and quantify a
clonotype. In other embodiments, the fragment that can be sequenced
is the full variable region. In yet another embodiment, the antigen
recognition region or the complementarity determining region 3
(CDR3) is sequenced. A fragment containing the full CDR3 or the
full variable region can be amplified to allow the sequencing of
the CDR3 comprising parts of the V, D, and J segments.
One or more tags on amplified products can be used for sequencing
immunoglobulin or T cell receptor genes. One or more primers that
anneal to the tags can be used in the sequencing reactions.
Different sections of an amplified molecule can be sequenced in
separate reactions, and the sequencing results can be pieced
together to generate a partial or a full sequence of the
molecule.
In one embodiment, only the CDR3 is amplified and sequenced.
Amplification and sequencing of the CDR3 can be accomplished by
using primers specific to one or more V segment sequences (as well
as one or more primer(s) on the other side of the amplicon in the C
segment). Primers for each of the V segments can be utilized in one
or more amplification reactions leading to the amplification of the
full repertoire of sequences. This repertoire of sequences can then
be mixed and subjected to separation, with or without
amplification, and sequenced using any of the sequencing techniques
described. When the amplification with the various V primers is
done in separate tubes, the number of molecules carrying the
different V segments can be "normalized" due to PCR saturation. For
example, if one particular V segment had one or several clonal
expansions leading to its representation more than other segments
this information may be erased or decreased since the PCR reaction
for each segment can be driven to saturation or close to it. Real
time PCR can be used to quantify how much of each V segment is
present. The full CDR3 can be sequenced, or a subset of the
sequence CDR3 can be sequenced.
In one embodiment, only a subset of clonotypes is analyzed. This
can be accomplished by amplifying with a primer specific to the
subset of clonotypes, for example, a primer that is specific to the
V segment. Unique clonotypes can be identified by sequencing with
long contiguous reads that provide full connectivity. In some
embodiments, when several sequences of interest are present, a
short read length across only one of the junctions can generate
degenerate tags that are not unique to a specific clonotype but are
shared among multiple clonotypes. For example sequencing across the
V/J junction can lump all the sequences with the same V/J
irrespective of the D segment as one clonotype. Information on the
full connectivity of all segments allows sequences to be
distinguished that may share the same V and J segments but are
connected to different D segments, for example.
The same analysis can be done when only the V and D are present
(e.g., the light chain of an antibody or the .alpha. subunit in
TCR). The full diversity of TCR and BCR incorporates both subunits.
However, it is possible to do the analysis on the sequences of both
subunits.
Errors generated by sequencing and/or by amplification can be taken
into account when generating the clonotype profile. For example,
see Example 5.
The initial amplification can be done from DNA or RNA (e.g., after
conversion to cDNA).
II. Methods for Determining Correlating Clonotypes, Disease
Activity Scores, and Algorithms for Determining Either or Both
A. Correlating Versus Non-Correlating Clonotypes
The vast repertoire of T and B cell receptor sequences creates a
challenge in finding individual cells that are correlated with
specific human health outcomes. In many cases the sequences of
clonotypes that will be of interest will be unique to the
individual being studied. The methods of the present invention
provide means for distinguishing a) correlating clonotypes (which
can be those clonotypes whose level correlate with disease) from b)
non-correlating clonotypes (which can be those clonotypes whose
levels do not correlate with disease). In one embodiment, a
correlating clonotype can display either positive or negative
correlation with disease. In another embodiment, a clonotype
present at a peak state of a disease but not present at a non-peak
state of a disease can be a correlating clonotype (positive
correlation with disease). In another embodiment, a clonotype that
is more abundant (i.e. is present at a higher level of molecules)
in a peak state (or stage) of a disease than at a non-peak state of
the disease can be a correlating clonotype (positive correlation
with the disease). In another embodiment, a clonotype absent at a
peak state of a disease but present during a non-peak state of the
disease can be a correlating clonotype (negative correlation with
disease). In another embodiment, a clonotype that is less abundant
at a peak state of a disease than at a non-peak state of a disease
can be a correlating clonotype (negative correlation with disease).
In another embodiment, a correlating clonotype for an individual is
determined by an algorithm.
B. Discovering Correlating and Non-Correlating Clonotypes Using a
Calibration Test without a Population Study
In this embodiment of the invention, correlating clonotypes are
identified by looking at the clonotypes present in some sample that
has relevance to a disease state (e.g., see FIG. 14). This state
could be blood from a sample at a peak state of disease (e.g. a
blood sample from an MS or lupus patient during an acute flare), or
affected tissue that is presumed to be enriched for T and B cells
involved in the disease for that individual. Examples of these
tissues could be kidney biopsies of lupus patients with kidney
inflammations, CSF in MS patients during a flare, synovial fluid
for rheumatoid arthritis patients, or tumor samples from cancer
patients. In all of these examples, it is likely that the tissues
will contain relevant T and B cells that are related to the disease
(though not necessarily the causative agents). It is notable that
if this method is used to identify the clonotypes that are relevant
to disease, they will only be relevant to the individual in whose
sample they were detected. As a result, a specific calibration test
will be needed in order to use this method to identify correlating
clonotypes in any given individual with a disease.
In one embodiment, a method for determining one or more correlating
clonotypes in a subject is provided. The method can include steps
for a) generating one or more clonotype profiles by nucleic acid
sequencing individual, spatially isolated molecules from at least
one sample from the subject, wherein the at least one sample is
related to a first state of the disease, and b) determining one or
more correlating clonotypes in the subject based on the one or more
clonotype profiles.
In one embodiment, at least one sample is from a tissue affected by
the disease. In another embodiment, said determination of one or
more correlating clonotypes comprises comparing clonotype profiles
from at least two samples. In another embodiment, the first state
of the disease is a peak state of the disease. In another
embodiment, one or more correlating clonotypes are present in the
peak state of the disease. In another embodiment, the one or more
correlating clonotypes are absent in the peak state of the disease.
In another embodiment, one or more correlating clonotypes are high
in the peak state of the disease. In another embodiment, one or
more correlating clonotypes are low in the peak state of the
disease. In another embodiment, the sample comprises T-cells and/or
B-cells. In another embodiment, the T-cells and/or B-cells comprise
a subset of T-cells and/or B-cells. In another embodiment, the
subset of T-cells and/or B-cells are enriched by interaction with a
marker. In another embodiment, the marker is a cell surface marker
on the subset of T-cells and/or B-cells. In another embodiment, the
subset of T-cells and/or B-cells interacts with an antigen
specifically present in the disease.
In one embodiment, the disease is an autoimmune disease. In another
embodiment, the autoimmune disease is systemic lupus erythematosus,
multiple sclerosis, rheumatoid arthritis, or Ankylosing
Spondylitis.
C. Discovering Correlating and Non-Correlating Clonotypes Using a
Population Study
In one embodiment, a method is provided for identifying correlating
clonotypes using a population study (e.g., see FIG. 15). The
utility of the population study is that it allows the specific
information about correlating clonotypes that have been ascertained
in individuals with known disease state outcomes to be generalized
to allow such correlating clonotypes to be identified in all future
subjects without the need for a calibration test. Knowledge of a
specific set of correlating clonotypes can be used to extract rules
about the likely attributes (parameters) of clonotypes that will
correlate in future subjects.
In one embodiment, the provided invention encompasses methods that
include identifying correlating and non correlating clonotypes by
sequencing the immune cell repertoire in a study of samples from
patients with disease(s) and optionally healthy controls at
different times and, in the case of the patients with a disease, at
different (and known) states of the disease course characterized by
clinical data. The disease can be, for example, an autoimmune
disease. The clonotypes whose level is correlated with measures of
disease in these different states can be used to develop an
algorithm that predicts the identity of a larger set of sequences
that will correlate with disease as distinct from those that will
not correlate with disease in all individuals. Unlike the case of
the calibration test, correlating sequences need not have been
present in the discovery study but can be predicted based on these
sequences. For example, a correlating sequence can be TCR gene DNA
sequence that encodes the same amino acid sequence as the DNA
sequence of a clonotype identified in the discovery study.
Furthermore, the algorithm that can predict one or more correlating
clonotypes can be used to identify clonotypes in a sample from any
individual and is in no way unique to a given individual, thus
allowing the correlating clonotypes to be predicted in a novel
sample without prior knowledge of the clonotypes present in that
individual.
In one aspect, a method for developing an algorithm that predicts
one or more correlating clonotypes in any sample from a subject
with a disease is provided comprising: a) generating a plurality of
clonotype profiles from a set of samples, wherein the samples are
relevant to the disease, b) identifying one or more correlating
clonotypes from the set of samples, c) using sequence parameters
and/or functional data from one or more correlating clonotypes
identified in b) to develop an algorithm that can predict
correlating clonotypes in any sample from a subject with the
disease.
In one embodiment, the set of samples are taken from one or more
tissues affected by the disease.
In another embodiment, the identifying one or more correlating
clonotypes comprises comparing clonotype profiles from at least two
samples. In another embodiment, the functional data include binding
ability of markers in T-cell and/or B-cells or interaction with
antigen by a T-cell or B cell. In another embodiment, said sequence
parameters comprise nucleic acid sequence and predicted amino acid
sequence. In another embodiment, the samples are from one or more
individuals at a peak stage of the disease. In another embodiment,
said one or more correlating clonotypes are present in the peak
state of the disease. In another embodiment, said one or more
correlating clonotypes are at a high level in the peak state of the
disease. In another embodiment, one or more correlating clonotypes
are at a low level in the peak state of the disease. In another
embodiment, one or more correlating clonotypes are absent at the
peak state of the disease.
In one embodiment, the disease is an autoimmune disease. In another
embodiment, the autoimmune disease is systemic lupus erythematosus,
multiple sclerosis, rheumatoid arthritis, or Ankylosing
Spondylitis.
In another aspect, a method for discovering one or more correlating
clonotypes for an individual is provided, comprising a) inputting a
clonotype profile from a sample from the individual into an
algorithm, and b) using the algorithm to determine one or more
correlating clonotypes for the individual. The algorithm can be an
algorithm developed by: a) generating a plurality of clonotype
profiles from a set of samples, wherein the samples are relevant to
the disease, b) identifying one or more correlating clonotypes from
the set of samples, and c) using sequence parameters and/or
functional data from one or more correlating clonotypes identified
in b) to develop the algorithm that can predict correlating
clonotypes in any sample from a subject with the disease.
D. Discovering Correlating and Non Correlating Clonotypes Using a
Calibration Test Combined with a Population Study
In one embodiment of the invention the correlating clonotypes are
identified by using a calibration test combined with a population
study (e.g., see FIG. 17). In this embodiment the population study
does not result in an algorithm that allows clonotypes to be
predicted in any sample but rather it allows an algorithm to be
developed to predict correlating clonotypes in any sample from a
subject for whom a particular calibration clonotype profile has
been generated (e.g., see FIG. 16). An example of this could be the
development of an algorithm that would predict the correlating
clonotypes in a lupus patient based on the clonotype profile
measured from a blood sample at any stage of disease after having
first having had a blood test taken during a clinical flare state
that was used to calibrate the algorithm.
In this embodiment the provided invention encompasses methods for
identifying correlating and non-correlating clonotypes by
sequencing the immune cell repertoire in a study of samples from
patients of disease(s) and optionally healthy controls at different
times and, in the case of the patients with a disease, at different
(and known) states of the disease course characterized by clinical
data. The clonotypes that are found at different frequency (or
level) in the first state than in the second state are then used to
develop an algorithm that predicts which of the sequences found in
the repertoires of each individual at the first disease state will
correlate with disease at the later state in each individual as
distinct from those that will not correlate with disease in that
individual. Unlike the case of the calibration test alone,
correlating sequences may be a subset of all the sequences found to
be different between disease states. It is also possible that
correlating clonotypes are not found in the calibration sample but
are predicted based on the algorithm to be correlating if they
appear in a future sample. As an example, a clonotype that codes
for the same amino acid sequence as a clonotype found in a
calibration sample may be predicted to be a correlating clonotype
based on the algorithm that results from the population study.
Unlike the previous embodiments, the algorithm is developed to
predict the correlating clonotypes based on a calibration clonotype
profile which is a clonotype profile generated in the individual
for whom the correlating clonotypes are to be predicted which at a
specific state of disease. In this embodiment the algorithm cannot
be used to generate correlating clonotypes in a particular
individual until a specific calibration clonotype profile has been
measured. After this calibration profile has been measured in a
particular subject, all subsequent correlating clonotypes can be
predicted based on the measurement of the clonotype profiles in
that individual.
In another aspect, a method for discovering one or more correlating
clonotypes for an individual is provided, comprising a) inputting a
clonotype profile from a sample from the individual into an
algorithm, and b) using the algorithm to determine one or more
correlating clonotypes for the individual. The algorithm can be an
algorithm developed by: a) generating a plurality of clonotype
profiles from a set of samples, wherein the samples are relevant to
the disease, b) identifying one or more correlating clonotypes from
the set of samples, and c) using sequence parameters and/or
functional data from one or more correlating clonotypes identified
in b) to develop an algorithm that can predict correlating
clonotypes in any sample from a subject with the disease. In one
embodiment, the sample is at taken at a peak state of disease. In
another embodiment, the sample is taken from disease affected
tissue.
E. Sequence Related Parameters that can be Used to Predict
Correlating Clonotypes
In order to conduct a population study a training set can be used
to understand the characteristics of correlating clonotypes by
testing various parameters that can distinguish those correlating
clonotypes from those that do not. These parameters include the
sequence or the specific V, D, and J segments used. In one
embodiment it is shown that specific V segments are more likely to
correlate with some diseases as is the case if the clonotypes for a
specific disease are likely to recognize related epitopes and hence
may have sequence similarity. Other parameters included in further
embodiments include the extent of hypersomatic mutation identified
and the level of a clonotype at the peak of an episode and its
level when the disease is relatively inactive. Other parameters
that may predict correlating clonotypes include without limitation:
1) sequence motifs including V or J region, a combination VJ, short
sequences in DJ region; 2) Sequence length of the clonotype; 3)
Level of the clonotype including absolute level (number of clones
per million molecules) or rank level; 4) Amino acid and nucleic
acid sequence similarity to other clonotypes: the frequency of
other highly related clonotypes, including those with silent
changes (nucleotide differences that code for same amino acids) or
those with conservative amino acid changes; 5) For the BCRs the
level of somatic mutations in the clonotype and/or the number of
distinct clonotypes that differ by somatic mutations from some
germline clonotypes; 6) clonotypes whose associated proteins have
similar 3 dimensional structures.
F. Functional Data to Refine the Determination of Correlating
Clonotypes
Further embodiments will make use of functional data to aid in
identifying correlating clonotypes. For example, T-cells and/or
B-cells containing certain markers that are enriched in cells
containing correlating clonotypes can be captured through standard
methods like FACS or MACS. In another embodiment the marker is a
cell-surface marker. In another embodiment T-cells and/or B-cells
reactivity to an antigen relevant to the pathology or to affected
tissue would be good evidence of the pathological relevance of a
clonotype.
In another embodiment the sequence of the candidate clonotypes can
be synthesized and put in the context of the full TCR or BCR and
assessed for the relevant reactivity. Alternatively, the amplified
fragments of the different sequences can be used as an input to
phage, ribosome, or RNA display techniques. These techniques can
select for the sequences with the relevant reactivity. The
comparison of the sequencing results for those before and after the
selection can identify those clones that have the reactivity and
hence are likely to be pathological. In another embodiment, the
specific display techniques (for example phage, ribosome, or RNA
display) can be used in an array format. The individual molecules
(or amplifications of these individual molecules) carrying
individual sequences from the TCR or BCR (for example CDR3
sequences) can be arrayed either as phages, ribosomes, or RNA.
Specific antigens can then be studied to identify the sequence(s)
that code for peptides that bind them. Peptides binding antigens
relevant to the disease are likely to be pathological.
G. Generating an Immune Load Algorithm
An algorithm can be used to compute an Immune Load (e.g., see FIG.
18). The Immune Load can be used to make a clinical decision. Using
data from an experiment, (e.g., an experiment comprising samples
from subjects in a first state of a disease and samples from
subjects in a second state of the disease), an algorithm can be
developed that combines the information about the levels of the
correlating and non-correlating clonotypes into a single score
(Immune Load). The parameters of this algorithm can then be
adjusted to maximize the correlation between Immune Load and the
clinical data. For example, the clinical data can be a clinical
measure of disease severity (e.g., the extent of lesions on an MRI
for a multiple sclerosis patient).
The correlating clonotypes used in generating a Immune Load
algorithm can be generated using a calibration test, a population
study, or a calibration test and a population study as described
above.
Some of the factors that can be considered in combining the
correlating clonotypes are the number of correlating clonotypes,
their level, their rate of change (velocity), and the rate of
change in the velocity (acceleration). Other factors to be assessed
include the level of the clonotypes at the episode peak and at the
inactive disease state
In one embodiment, the Immune Load generated relates to an
autoimmune disease. Such a Load can be referred to as an AutoImm
Load.
In one aspect, a method for generating an algorithm that calculates
a disease activity score is provided, comprising: a) developing an
algorithm that uses a set of factors to combine levels of
correlating clonotypes into a disease activity score, b) comparing
the disease activity score to clinical data regarding the disease
state, and c) optimizing the factors in order to maximize the
correlation between clinical data and the disease activity
score.
H. Monitoring Disease Using the Load Algorithm
1. Monitoring Disease without a Calibration Test
In one embodiment of the invention the clonotypes and the Immune
Load algorithm are determined using a population study (e.g., see
FIG. 19). Immune Load can be used directly without having to first
calibrate the individual patient. This test can be done when the
patient is in any disease state. This test can be used to generate
specific correlating and non-correlating clonotypes based on the
algorithm developed above. Immune Load can then be calculated using
the second algorithm generated in a population study. This score
can then be used clinically.
In another aspect, a method for monitoring the disease state of a
individual is provided comprising: a) determining a clonotype
profile from a sample from a subject, b) inputting the clonotype
profile information from a) into an algorithm, and c) using the
algorithm to generate a score predictive of the disease state of
the individual. The algorithm can be an algorithm generated by a)
developing an algorithm that uses a set of factors to combine
levels of correlating clonotypes into a disease activity score, b)
comparing the disease activity score to clinical data regarding the
disease state, and c) optimizing the factors in order to maximize
the correlation between clinical data and the disease activity
score.
2. Monitoring Disease Using a Calibration Test
In one embodiment of the provided invention the correlating
clonotypes and the Immune Load algorithm are determined using a
calibration test or calibration test and a population study (e.g.,
see FIG. 20). Immune Load can be used in the clinic by first
conducting a calibration test. This test can be done when the
patient is in a state which is similar to the first state used in
the study that generated the correlating and non-correlating
clonotypes that are used in the Immune Load algorithm. For example,
this state can be a flare state of an autoimmune disease if this is
how the Immune Load algorithm was derived. This calibration test
can then be used to generate the specific correlating and
non-correlating clonotypes to be used in the subsequent disease
monitoring tests. At a later point in the treatment of this
patient, another test is done on the patient and Immune Load can be
calculated using the algorithm generated in the discovery study,
and the list of clonotype levels generated in this patient's
specific calibration test. This Immune Load score can then be used
clinically.
In another aspect, a method for monitoring the disease state of a
individual is provided comprising: a) determining a clonotype
profile from a sample from a subject, b) inputting the clonotype
profile information from a) into an algorithm, and c) using the
algorithm to generate a score predictive of the disease state of
the individual. The algorithm can be an algorithm generated a)
developing an algorithm that uses a set of factors to combine
levels of correlating clonotypes into a disease activity score, b)
comparing the disease activity score to clinical data regarding the
disease state, and c) optimizing the factors in order to maximize
the correlation between clinical data and the disease activity
score. In another embodiment, the method can further comprise
determining one or more correlating clonotypes in the individual by
any of the methods of the provided invention, and inputting
information the one or more correlating clonotypes into the
algorithm.
In one embodiment, the disease is an autoimmune disease. In another
embodiment, the autoimmune disease is systemic lupus erythematosus,
multiple sclerosis, rheumatoid arthritis, or Ankylosing
Spondylitis.
3. Other Factors Related to the Use of Immune Load
The same Immune Load may mean different things for different
patients. For one, the full clinical picture of a patient needs to
be considered. From a testing perspective, one may consider the
velocity (rate of change of Immune Load over time) and acceleration
(rate of change of velocity over time) in addition to the level of
Immune Load in making clinical decisions. For example if the
AutoImm Load score is increasing (high velocity) it may be
predictive of an incipient flare in an autoimmune disease.
Additional tests that can be integrated in the Load score, for
example, an AutoImm Load score, include, for example, erythrocyte
sedimentation rate (ESR), C-reactive protein (CRP) levels, Anti-ds
DNA, other autoantibody titers, complement levels, urine protein
levels, Urine protein/creatinine ratio, creatinine levels, blood
urea nitrogen (BUN) levels, platelet levels, WBC counts,
hematorcrit (Hct), Hb, urinalysis results. Other tests that are
related to SLE that can be integrated include, for example, CD27
level, CD27++ cell level, INF-responsive genes (Baechler, E C et
al. (2003) Proc. Natl. Acad. Sci. 100: 2610-2615), and chemokine
score (Bauer J W et al. (2009) Arthritis Rheum. 60:3098-3107).
Other tests not related to lupus include, for example,
thyroid-stimulating hormone (TSH) test, triiodothyronine (T3) test,
thyroxine (T4) test, liver function tests (LFTs), other
autoantibodies, calprotectin test, lactoferrin test, and synovial
fluid analysis. The additional tests can include imaging test,
including, for example, MRI, CT-scan, X-ray, and ultrasound.
III. Determining Disease States
Because the immune system is so central to human health, the
ability to measure immune responses has wide applications in
medicine. This invention teaches the ability to use the immune
system to understand underlying disease state when it is mediated
by the immune system. This allows a very powerful set of diagnostic
and prognostic applications that use the immune profiles to inform
the risks of wide variety of clinical outcomes and allow physicians
to intervene more effectively.
A. Utility of Immune Profiling in Autoimmune Disease Treatment
The methods of the provided invention can be used to diagnose and
treat autoimmune disease in a subject. Autoimmune disease involves
adaptive immune cells escaping the usual process conferring
autoimmunity and attacking some target(s) on bodily tissue.
Autoimmune diseases include, for example, acute disseminated
encephalomyelitis, Addison's disease, ankylosing spondylitis,
antiphospholipid antibody syndrome, autoimmune hemolytic anemia,
autoimmune hepatitis, autoimmune inner ear disease, Behcet's
disease, bullous pemphigoid, Celiac disease, Chagas disease,
Chronic obstructive pulmonary disease, dermatomyositis, diabetes
mellitus type 1, Goodpasture's syndrome, Graves' disease,
Guillain-Barre syndrome, Hashimoto's thyroditis, Hidradenitis
suppurativa, Idiopathic thrombocytopenic purpura, Interstitial
cystitis, multiple sclerosis, myasthenia gravis, neuromyotonia,
pemphigus vulgaris, pernicious anemia, polymyositis, primary
biliary cirrhosis, rheumatoid arthritis, scleroderma, systemic
lupus erythematosus, Sjogren's syndrome, and vasculitis syndromes.
The stages of these autoimmune diseases can be diagnosed using the
methods of the provided invention. Treatments can be suggested to a
subject based on the stage of the autoimmune disease.
Clinical information regarding a subject with an autoimmune
disease, or suspected of having an autoimmune disease, can be used
to determine the disease state (or AutoImm load). Clinical
information can be used to identify patterns of a clonotype profile
that correlate with a disease state. Clinical information can
include, for example, height, weight, eye color, age, gender,
ethnic group, blood pressure, LDL cholesterol levels, HDL
cholesterol levels, family medical history, and molecular marker
information.
Clinical information can include symptoms of one or more autoimmune
diseases. For autoimmune hepatitis symptoms can include fatigue,
hepatomegaly, jaundice, pruritus, skin rash, arthralgia, abdominal
discomfort, spider angiomas, nausea, vomiting, anorexia, dark
urine, pale or gray stools. For dermatoymyositis (DM), symptoms can
include rash (patchy, bluish-purple discolorations on the face,
neck, shoulders, upper chest, elbows, knees, knuckles and back)
accompanying or preceding muscle weakness, dysphagia, myalgia,
fatigue, weight loss and low-grade fever. For Graves' disease,
symptoms can include weight loss due to increased energy
expenditure, increased appetite, heart rate and blood pressure, and
tremors, nervousness and sweating. For Hashimoto's thyroiditis,
symptoms can include mental and physical slowing, greater
sensitivity to cold, weight gain, coarsening of the skin, goiter.
For mixed connective tissue disease (MCTD)), symptoms can include
features of systemic lupus erythematosus (SLE), scleroderma and
polymyositis. For Pemphigoid, bullous (BP) symptoms can include
mildly pruritic welts to severe blisters and infection, oral or
esophageal bullae. For pemphigus, symptoms can include blistering
of skin and mucous membranes. For pernicious anemia, symptoms can
include shortness of breath, fatigue, pallor, tachycardia,
inappetence, diarrhea, tingling and numbness of hands and feet,
sore mouth and unsteady gait. For polymyositis (PM), symptoms can
include muscle weakness, dysphagia and myalgia. For primary biliary
cirrhosis (PBC), symptoms can include fatigue and pruritus. For
scleroderma (systemic sclerosis), symptoms can include swelling and
puffiness of the fingers or hands, skin thickening, skin ulcers on
the fingers, joint stiffness in the hands, pain, sore throat and
diarrhea. For Sjogren's syndrome, symptoms can include dryness of
the eyes and mouth, swollen neck glands, difficulty swallowing or
talking, unusual tastes or smells, thirst and tongue ulcers. For
systemic lupus erythematosus (SLE)), symptoms can include fever,
weight loss, hair loss, mouth and nose sores, malaise, fatigue,
seizures and symptoms of mental illness, joint inflammation similar
to RA, butterfly rash on nose and cheeks, extreme sensitivity to
cold in the hands and feet. For vasculitis syndromes, e.g.,
Wegener's granulomatosis, idiopathic crescentic glomerulonephritis
(ICGN), microscopic polyarteritis (MPA), pulmonary renal syndrome
(PRS), symptoms can include fatigue, weakness, fever, arthralgia,
abdominal pain, renal problems and neurological problems. The
clinical information can be from one or more subjects at one or
more points of time.
The clinical information can include information regarding
responses of a subject with an autoimmune disease to one or more
treatments the subject has received.
The clinical utility of AutoImm Load is discussed for specific
autoimmune diseases below. Another embodiment of this invention
contemplates the combination of the immune profiling tests with
other markers that are already in use for the detection of disease
activity in these diseases to allow tests with greater sensitivity
and specificity. Other molecular identifiers or markers can be used
in computing the AutoImm Load or for determining the disease state.
Molecular identifiers can include nucleic acids, proteins,
carbohydrates, and lipids, and expression profiles of nucleic acids
or proteins. The molecular identifiers can be of human or non-human
origin (e.g., bacterial). The identifiers or markers can be
determined by techniques that include, for example, comparative
genomic hybridization (CGH), chromosomal microarray analysis (CMA),
expression profiling, DNA microarray, high-density oligonucleotide
microarray, whole-genome RNA expression array, peptide microarray,
enzyme-linked immunosorbent assay (ELISA), genome sequencing, copy
number (CNV) analysis, small nucleotide polymorphism (SNP)
analysis, immunohistochemistry, in-situ hybridization, fluorescent
in-situ hybridization (FISH), PCR, Western blotting, Southern
blotting, SDS-PAGE, gel electrophoresis, and Northern blotting.
For systemic lupus erythematosus, markers can include levels of
erythrocyte sedimentation rate (ESR), C-reactive protein (CRP)
levels, Anti-ds DNA, other autoantibody titers, complement levels,
urine protein levels, Urine protein/creatinine ratio, creatinine
levels, blood urea nitrogen (BUN) levels, platelet levels, WBC
counts, hematocrit (Hct), Hb, and urinalysis results. Other tests
that are related for instance to SLE that can be integrated
include, for example, CD27 level, CD27++ cell level, INF-responsive
genes, and chemokine score.
1. Systemic Lupus Erythematosus (SLE)
The methods of the provided invention can be used to determine
states or stages of systemic lupus erythematosus (SLE or lupus).
SLE is a serious autoimmune condition that often afflicts young
adults (mostly females). It is characterized by inflammatory
processes that can affect many organs including the skin, joints,
kidneys, lungs, heart, and central nervous system leading to
frequent disabilities and sometimes death. The disease follows a
very unpredictable course marked by flare periods followed by
quiescent periods of remission. Nevertheless, patients diagnosed
with SLE are seen regularly by a rheumatologist and treated with a
variety of serious medications. These medications include steroids
such as Prednisone and other immunosuppressants such as Cellcept
(mycophenolate mofetil). While these drugs can reduce organ damage
they contain significant side effects including risk of infection
and infertility. The unreliability for some of the symptoms (e.g.,
pain and fatigue) and the unpredictable disease course makes
tailoring medication doses difficult, resulting in art
overtreatment of some patients and under-treatment of others. As a
result, the treatment of SLE poses significant therapeutic
challenges to the clinician.
There are a number of standard methods a clinician can use to
assess the activity of SLE. The status of the disease can be
measured by observing the clinical symptoms of the disease. These
methods include assessment of signs (e.g., skin rash) and symptoms
(e.g., joint pain and fatigue) as well as lab results (e.g., urine
protein/creatinine ratio, anti-ds DNA antibody, and blood counts).
These clinical markers, however, can be lagging indicators of
disease status and as such patients may respond only after weeks or
months of therapy. Furthermore, in some cases symptoms can be
difficult to assess with precision (e.g., pain and fatigue). Other
markers of inflammation, for example anti-ds DNA antibody,
complement level (e.g., C3), C reactive protein (CRP), and
erythrocyte sedimentation rate (ESR) usually lack specificity
and/or sensitivity. Invasive methods such as kidney biopsy are
impractical for routine use. As a result clinicians perform quite a
frequent testing of their patients without a perfect measure of the
disease status. The clinical symptoms and laboratory assessment are
integrated in measures such as Systemic Lupus Erythematosus Disease
Activity Index (SLEDAI) and Physician Global Assessment (PGA).
These measures are not done routinely in clinical practice and
often fall short in several clinical situations.
Specific examples of the utility of AutoImm Load in making
therapeutic interventions in SLE are discussed in greater detail in
the examples section along with specific enabling studies that
determine AutoImm Load.
2. Multiple Sclerosis (MS)
The methods of the provided invention can also be used to determine
states or stages of Multiple Sclerosis (MS). MS is an autoimmune
disease that affects the brain and spinal cord (central nervous
system). Symptoms vary, because the location and severity of each
attack can be different. Episodes can last for days, weeks, or
months. These episodes alternate with periods of reduced or no
symptoms (remissions). It is common for the disease to return
(relapse). However, the disease may continue to get worse without
periods of remission.
Because nerves in any part of the brain or spinal cord may be
damaged, patients with multiple sclerosis can have symptoms in many
parts of the body. Muscle symptoms include, for example, loss of
balance, numbness or abnormal sensation in any area, pain because
of muscle spasms, pain in the arms or legs, problems moving arms or
legs, problems walking, problems with coordination and making small
movements, slurred or difficult-to-understand speech, tremor in one
or more arms or legs, uncontrollable spasm of muscle groups (muscle
spasticity), and weakness in one or more arms or legs.
Eye symptoms include, for example, double vision, eye discomfort,
uncontrollable rapid eye movements, and vision loss (usually
affects one eye at a time).
Other brain and nerve symptoms include, for example, decreased
attention span, decreased judgment, decreased memory, depression or
feelings of sadness, dizziness and balance problems, facial pain,
hearing loss, and fatigue.
Bowel and bladder symptoms include, for example, constipation,
difficulty beginning urinating, frequent need to urinate, stool
leakage, strong urge to urinate, and urine leakage
(incontinence).
There is no known cure for multiple sclerosis at this time.
However, there are therapies that may slow the disease. The goal of
treatment is to control symptoms and help the patient maintain a
normal quality of life.
Medications used to slow the progression of multiple sclerosis can
include, for example, immune modulators to help control the immune
system, including interferons (Avonex, Betaseron, or Rebif),
monoclonal antibodies (Tysabri), glatiramer acetate (Copaxone),
mitoxantrone (Novantrone), methotrexate, azathioprine (Imuran),
cyclophosphamide (Cytoxan), and natalizumab (Tysabri). Steroids can
be used to decrease the severity of attacks.
Medications to control symptoms can include, for example, medicines
to reduce muscle spasms such as Lioresal (Baclofen), tizanidine
(Zanaflex), or a benzodiazepine, cholinergic medications to reduce
urinary problems, antidepressants for mood or behavior symptoms,
and amantadine for fatigue.
MS affects women more than men. The disorder most commonly begins
between ages 20 and 40, but can be seen at any age. MS is caused by
damage to the myelin sheath, the protective covering that surrounds
nerve cells. When this nerve covering is damaged, nerve impulses
are slowed down or stopped. MS is a progressive disease, meaning
the nerve damage (neurodegeneration) gets worse over time. How
quickly MS gets worse varies from person to person. The nerve
damage is caused by inflammation. Inflammation occurs when the
body's own immune cells attack the nervous system. Repeated
episodes of inflammation can occur along any area of the brain and
spinal cord. Researchers are not sure what triggers the
inflammation. The most common theories point to a virus or genetic
defect, or a combination of both. MS is more likely to occur in
northern Europe, the northern United States, southern Australia,
and New Zealand than in other areas. Geographic studies indicate
there may be an environmental factor involved. People with a family
history of MS and those who live in a geographical area with a
higher incidence rate for MS have a higher risk of the disease.
Symptoms of MS may mimic those of many other nervous system
disorders. The disease is diagnosed by ruling out other conditions.
People who have a form of MS called relapsing-remitting may have a
history of at least two attacks, separated by a period of reduced
or no symptoms. The health care provider may suspect MS if there
are decreases in the function of two different parts of the central
nervous system (such as abnormal reflexes) at two different times.
A neurological exam may show reduced nerve function in one area of
the body, or spread over many parts of the body.
Tests to diagnose multiple sclerosis include, for example,
cerebrospinal fluid tests, including CSF oligoclonal banding, head
MRI scan, lumbar puncture (spinal tap), nerve function study
(evoked potential test), and spine MRI.
Like other autoimmune diseases, MS follows an unpredictable course
with acute flares and periods of remission. There are increasing
numbers of therapies, each with side effects that range from
serious (weight gain and depression) to life threatening
(pancytopenia and PML infections), variable effectiveness in
different patients, and high costs. At the same time, the lack of
highly accurate and specific routine tests of MS disease activity
make the challenge of effectively administering therapy
complicated. Clinical episodes can be separated by long time
periods (up to years in early stage disease) even without
treatment. In addition, available medications reduce the likelihood
of relapse but do not completely prevent them. Therefore disease
activity is difficult to assess and thus, there is an inadequate
short term measure of disease activity that could be used to
measure whether a specific therapy is showing efficacy in a given
patient by measuring the reduction in number or severity of
relapses. The only other test available for monitoring disease
activity is brain MRI to track the state of lesions as revealed
with the aid of contrast enhancing agents such as gadolinium.
However, such imaging offers only an integrated view of brain
damage and lacks specificity and time resolution. Attempting to use
MRI imaging to follow disease course on time scales shorter than a
year is impractical given the costs, the lack of specificity and
the dangers of excessive contrast exposure. As a result, patients
are often treated at great expense for prolonged periods of time
without any effective feedback that would allow the physician to
modify dosing and/or switch of add therapies.
3. Rheumatoid Arthritis (RA)
The methods can be used to measure disease status for Rheumatoid
arthritis patients. Rheumatoid arthritis (RA) is a chronic,
systemic inflammatory disorder that can affect many tissues and
organs but principally attacks the joints, producing an
inflammatory synovitis that often progresses to destruction of the
articular cartilage and ankylosis of the joints. Rheumatoid
arthritis can also produce diffuse inflammation in the lungs,
pericardium, pleura, and sclera, and also nodular lesions, most
common in subcutaneous tissue under the skin. Although the cause of
rheumatoid arthritis is unknown, autoimmunity plays a pivotal role
in its chronicity and progression.
About 1% of the world's population is afflicted by rheumatoid
arthritis, women three times more often than men. Onset is most
frequent between the ages of 40 and 50, but people of any age can
be affected. It can be a disabling and painful condition, which can
lead to substantial loss of functioning and mobility. RA is
diagnosed chiefly on symptoms and signs, but can also be diagnosed
with blood tests (especially a test called rheumatoid factor) and
X-rays. Diagnosis and long-term management are typically performed
by a rheumatologist, an expert in the diseases of joints and
connective tissues.
Various treatments are available. Non-pharmacological treatment
includes physical therapy, orthoses, and occupational therapy.
Analgesia (painkillers) and anti-inflammatory drugs, including
steroids, can be used to suppress the symptoms, while
disease-modifying antirheumatic drugs (DMARDs) can be used to
inhibit or halt the underlying immune process and prevent long-term
damage. In recent times, the newer group of biologics has increased
treatment options
When RA is clinically suspected, immunological studies can be
performed, such as testing for the presence of rheumatoid factor
(RF, a specific antibody). A negative RF does not rule out RA;
rather, the arthritis is called seronegative. This is the case in
about 15% of patients. During the first year of illness, rheumatoid
factor is more likely to be negative with some individuals
converting to seropositive status over time. RF is also seen in
other illnesses, for example Sjogren's syndrome, and in
approximately 10% of the healthy population, therefore the test is
not very specific.
Because of this low specificity, new serological tests have been
developed, which test for the presence of so called
anti-citrullinated protein antibodies (ACPAs). Like RF, these tests
are positive in only a proportion (67%) of all RA cases, but are
rarely positive if RA is not present, giving it a specificity of
around 95%. As with RF, there is evidence for ACPAs being present
in many cases even before onset of clinical disease.
The most common tests for ACPAs are the anti-CCP (cyclic
citrullinated peptide) test and the Anti-MCV assay (antibodies
against mutated citrullinated Vimentin). Recently, a serological
point-of-care test (POCT) for the early detection of RA has been
developed. This assay combines the detection of rheumatoid factor
and anti-MCV for diagnosis of rheumatoid arthritis and shows a
sensitivity of 72% and specificity of 99.7%.
Also, several other blood tests can be done to allow for other
causes of arthritis, such as lupus erythematosus. The erythrocyte
sedimentation rate (ESR), C-reactive protein, full blood count,
renal function, liver enzymes and other immunological tests (e.g.,
antinuclear antibody/ANA) are all performed at this stage. Elevated
ferritin levels can reveal hemochromatosis, a mimic RA, or be a
sign of Still's disease, a seronegative, usually juvenile, variant
of rheumatoid.
The term Disease modifying anti-rheumatic drug (DMARD) originally
meant a drug that affects biological measures such as ESR and
hemoglobin and autoantibody levels, but is now usually used to mean
a drug that reduces the rate of damage to bone and cartilage.
DMARDs have been found both to produce durable symptomatic
remissions and to delay or halt progression. This is significant,
as such damage is usually irreversible. Anti-inflammatories and
analgesics improve pain and stiffness but do not prevent joint
damage or slow the disease progression.
There is an increasing recognition among rheumatologists that
permanent damage to the joints occurs at a very early stage in the
disease. In the past it was common to start therapy with just an
anti-inflammatory drug, and assess progression clinically and using
X-rays. If there was evidence that joint damage was starting to
occur, then a more potent DMARD would be prescribed. Ultrasound and
MRI are more sensitive methods of imaging the joints and have
demonstrated that joint damage occurs much earlier and in more
sufferers than was previously thought. People with normal X-rays
will often have erosions detectable by ultrasound that X-ray could
not demonstrate. The aim now is to treat before damage occurs.
There may be other reasons why starting DMARDs early is beneficial
to preventing structural joint damage. From the earliest stages of
the disease, the joints are infiltrated by cells of the immune
system that signal to one another in ways that may involve a
variety of positive feedback loops (it has long been observed that
a single corticosteroid injection may abort synovitis in a
particular joint for long periods). Interrupting this process as
early as possible with an effective DMARD (such as methotrexate)
appears to improve the outcome from the RA for years afterwards.
Delaying therapy for as little as a few months after the onset of
symptoms can result in worse outcomes in the long term. There is
therefore considerable interest in establishing the most effective
therapy with early arthritis, when the patient is most responsive
to therapy and have the most to gain.
Traditional small molecular mass drugs used to treat arthritis
include, for example, chemically synthesized DMARDs: azathioprine,
ciclosporin (cyclosporine A); D-penicillamine, gold salts,
hydroxychloroquine, leflunomide, methotrexate (MTX), minocycline,
and sulfasalazine (SSZ). Cytotoxic drugs include
Cyclophosphamide.
The most common adverse events relate to liver and bone marrow
toxicity (MTX, SSZ, leflunomide, azathioprine, gold compounds,
D-penicillamine), renal toxicity (cyclosporine A, parenteral gold
salts, D-penicillamine), pneumonitis (MTX), allergic skin reactions
(gold compounds, SSZ), autoimmunity (D-penicillamine, SSZ,
minocycline) and infections (azathioprine, cyclosporine A).
Hydroxychloroquine may cause ocular toxicity, although this is
rare, and because hydroxychloroquine does not affect the bone
marrow or liver it is often considered to be the DMARD with the
least toxicity. Unfortunately hydroxychloroquine is not very
potent, and is usually insufficient to control symptoms on its
own.
Biological agents (biologics) can be produced through genetic
engineering, and include, for example, tumor necrosis factor alpha
(TNF.alpha.) blockers--etanercept (Enbrel), infliximab (Remicade),
adalimumab (Humira), Interleukin 1 (IL-1) blockers--anakinra
(Kineret), monoclonal antibodies against B cells--rituximab
(Rituxan), T cell costimulation blocker--abatacept (Orencia),
Interleukin 6 (IL-6) blockers--tocilizumab (an anti-IL-6 receptor
antibody) (RoActemra, Actemra)
Anti-inflammatory agents include, for example, glucocorticoids,
Non-steroidal anti-inflammatory drugs (NSAIDs, most also act as
analgesics). Analgesics include, for example, paracetamol
(acetaminophen in US and Canada), opiates, diproqualone, and
lidocaine topical.
The challenge of treating RA lies in the fact that the disease is a
long term chronic illness with that can result in challenging
disability for which a large range of treatments exist each of
which has significant drawbacks. Many of the DMARDs subject the
patients to significant side effects including increased risk for
serious infections, cancer, or even autoimmune disease.
Furthermore, the biologically derived drugs are very expensive, and
the patient be subjected to frequent injections.
A doctor initiating therapy for a patient faces many possible
options. It would be desirable to get rapid feedback once a patient
starts therapy to understand whether the patient is responding to
the therapy that is chosen before the clinical manifestation
presents itself. Imaging is not sensitive and is expensive and many
blood markers such as CRP lack sufficient sensitivity. A test that
would allow the physician to rapidly determine the state of the
disease would allow him or her to adjust the therapy quickly to a
more effective therapy, saving the patient from additional joint
damage and more effectively using the expensive therapies
available.
A patient that has not experienced any acute flares since beginning
treatment may in fact still be experiencing ongoing inflammatory
damage to the joints that has not manifested itself clinically. A
test that would allow the doctor to differentiate this state from
the background would allow the therapy to be adjusted to try to
bring the patient closer to a state in which no ongoing joint
damage is being experienced.
Specific examples of how AutoImm Load can be used in managing MS
patients are described in further detail in the examples section of
this document.
4. Ankylosing Spondylitis
The methods can be used to detect disease activity for Ankylosing
spondylitis. Ankylosing spondylitis (AS, from Greek ankylos, bent;
spondylos, vertebrae), previously known as Bechterew's disease,
Bechterew syndrome, and Marie Strumpell disease, a form of
Spondyloarthritis, is a chronic, inflammatory arthritis and
autoimmune disease. It mainly affects joints in the spine and the
sacroilium in the pelvis, causing eventual fusion of the spine. It
is a member of the group of the spondyloarthropathies with a strong
genetic predisposition. Complete fusion results in a complete
rigidity of the spine, a condition known as bamboo spine.
The typical patient is a young male, aged 18-30, when symptoms of
the disease first appear, with chronic pain and stiffness in the
lower part of the spine or sometimes the entire spine, often with
pain referred to one or other buttock or the back of thigh from the
sacroiliac joint. Men are affected more than women by a ratio about
of 3:1, with the disease usually taking a more painful course in
men than women. In 40% of eases, ankylosing spondylitis is
associated with an inflammation of the eye (iridocyclitis and
uveitis), causing redness, eye pain, vision loss, floaters and
photophobia. Another common symptom is generalised fatigue and
sometimes nausea. Less commonly aortitis, apical lung fibrosis and
ectasia of the sacral nerve root sheaths may occur. As with all the
seronegative spondyloarthropathies, lifting of the nails
(onycholysis) may occur
There is no direct test to diagnose AS. A clinical examination and
X-ray studies of the spine, which show characteristic spinal
changes and sacroiliitis, are the major diagnostic tools. A
drawback of X-ray diagnosis is that signs and symptoms of AS have
usually been established as long as 8-10 years prior to
X-ray-evident changes occurring on a plain film X-ray, which means
a delay of as long as 10 years before adequate therapies can be
introduced. Options for earlier diagnosis are tomography and
magnetic resonance imaging of the sacroiliac joints, but the
reliability of these tests is still unclear. The Schober's test is
a useful clinical measure of flexion of the lumbar spine performed
during examination.
During acute inflammatory periods, AS patients will sometimes show
an increase in the blood concentration of C-reactive protein (CRP)
and an increase in the erythrocyte sedimentation rate (ESR), but
there are many with AS whose CRP and ESR rates do not increase so
normal CRP and ESR results do not always correspond with the amount
of inflammation a person actually has. Sometimes people with AS
have normal level results, yet are experiencing a significant
amount of inflammation in their bodies.
Ankylosing spondylitis (AS, from Greek ankylos, bent; spondylos,
vertebrae), previously known as Bechterew's disease, Bechterew
syndrome, and Marie Strumpell disease, a form of Spondyloarthritis,
is a chronic, inflammatory arthritis and autoimmune disease. It
mainly affects joints in the spine and the sacroilium in the
pelvis, causing eventual fusion of the spine.
It is a member of the group of the spondyloarthropathies with a
strong genetic predisposition. Complete fusion results in a
complete rigidity of the spine, a condition known as bamboo
spine.
There are three major types of medications used to treat ankylosing
spondylitis: 1) Anti-inflammatory drugs, which include NSAIDs such
as ibuprofen, phenylbutazone, indomethacin, naproxen and COX-2
inhibitors, which reduce inflammation and pain Opioid analgesics
have also been proven by clinical evidence to be very effective in
alleviating the type of chronic pain commonly experienced by those
suffering from AS, especially in time-release formulations. 2)
DMARDs such as ciclosporin, methotrexate, sulfasalazine, and
corticosteroids, used to reduce the immune system response through
immunosuppression; 3) TNF.alpha. blockers (antagonists) such as
etanercept, infliximab and adalimumab (also known as biologics),
are indicated for the treatment of and are effective
immunosuppressants in AS as in other autoimmune diseases;
TNF.alpha. blockers have been shown to be the most promising
treatment, slowing the progress of AS in the majority of clinical
cases, helping many patients receive a significant reduction,
though not elimination, of their inflammation and pain. They have
also been shown to be highly effective in treating not only the
arthritis of the joints but also the spinal arthritis associated
with AS. A drawback, besides the often high cost, is the fact that
these drugs increase the risk of infections. For this reason, the
protocol for any of the TNF-.alpha. blockers include a test for
tuberculosis (like Mantoux or Heaf) before starting treatment. In
case of recurrent infections, even recurrent sore throats, the
therapy may be suspended because of the involved immunosuppression.
Patients taking the TNF medications are advised to limit their
exposure to others who are or may be carrying a virus (such as a
cold or influenza) or who may have a bacterial or fungal
infection.
AS affects produces symptoms that are very common in the healthy
populations. For example, a patient presenting complaining of
severe back pain need not be experiencing an AS flare but rather
might just have routine back pain. The physician is forced to make
a decision about whether to treat these symptoms with expensive
drugs with potentially severe side effects without a very precise
view into the state of the disease. CRP and ESR do not provide a
very precise view of the disease status. At the same time the
course of the untreated disease can result in debilitating long
term spinal damage. This state of affairs leads to a difficult
clinical challenge and significant overtreatment is used. The
availability of an objective measure that reflects disease activity
can be of great help in the management of AS patients.
B. Utility of Immune Profiling in Cancer Detection
These methods can be used to measure cancer risk. Cancer has become
the leading cause of death in the industrialized world. Therefore
methods of treatment of cancer are in great need. Many approaches
for cancer treatment are being attempted including the development
of new small molecule drugs as well as antibodies targeting the
tumor.
One set of methods that has been proposed is immunotherapy. Tumor
surveillance is one of the functions of cells of the immune system.
There are several categories of tumor antigens that are recognized
by the immune system. The first category is comprised of antigens
that are novel generated by somatic mutation (point mutation or a
translocation) in the tumor. Another category consists of antigens
from proteins that are only expressed in male germ cells that do
not express MHC molecules. The dysregulation of gene expression in
many tumors may allow some of these antigens to be expressed. A
third category includes antigens from proteins only expressed in
particular tissues. The fourth category comprises antigens that are
significantly overexpressed in the tumor tissue. Finally the fifth
category includes antigens that result from abnormal
posttranslational modification.
One of the properties of tumors is their ability to escape
effective elimination by the immune system. It is thought that new
mutations acquired in the tumor allow it to go from the equilibrium
phase (where the tumor is not completely eliminated but its growth
is held in check) to the escape phase where the tumor grows without
effective control by the immune system. There are many mechanisms
that tumors employ to escape the immune system. These mechanisms
include the lack of specific antigenic peptides, or the
co-stimulatory molecules that can activate T cells. Other
mechanisms include the tumor secretion of factor that inhibit T
cells and the creation of a tumor-induced privileged site by
creating a physical barrier separating the tumor from lymphocytes.
Inducing the immune system to better fight the tumor as a strategy
for treating cancer is being studied and tested in multiple ways.
One approach is the adoptive T cell therapy. This approach focuses
on identifying T cells that are targeting tumor antigens through
isolation of cells that are infiltrating the tumor and/or reacting
to a specific tumor antigen. These T cells can be grown in vitro in
conditions that enhance their effectiveness, like the use of IL-2
and/or antigen-presenting cells. The expanded cells are then
infused back to the patient blood. Another approach is to use of
retrovirus containing tumor-specific TCR. These retrovirus can be
infused in the patient in special cells that later secrete the
retrovirus allowing it to infect T cells that then start expressing
the tumor-specific TCR. Finally a common approach is the use of
vaccination. The premise of this approach of therapy is that
immunization of the patient with one or more of the tumor antigens
will stimulate the immune system ability to fight the tumor.
Immunization is often done with the use of an adjuvant like Bacille
Calmette-Guerin (BCG). This approach has been successful in
preventing viral-induced cancer as evident by the ability to
prevent cervical cancers induced by HPV-16 and HPV-18. However this
has been less successful in the treatment of other tumors.
Much of the improvement in mortality because of cancer has come
about due to the availability of better early detection methods
leading for instance to reduced rates of mortality in breast cancer
and cervical cancers. The mutability of tumors makes their early
treatment much more effective than when they are detected late.
Traditionally, looking for cancer detection biomarkers usually
involved looking for markers that are highly expressed in the
cancer and are at low level or absent in the normal tissue. This
has led to the identification of several tumor markers, like PSA.
One problem with early detection of in cancer is that the greatest
value in for cancer detection occurs when detection of biomarker is
most difficult, i.e., the tumor is very small. Therefore in order
to have an effective cancer detection biomarker that can
distinguish patients with small tumors from those that do not,
there needs to be a tremendous difference in expression between the
tumor and the normal tissue due to the large difference in size
between the tumor and the normal tissue. Additionally the marker
needs to "spill" efficiently to the blood or other body fluid to
allow detection using a non-invasive technique.
This invention teaches a novel mechanism for cancer detection using
the immune cell response. In this view cancer detection is not
achieved by the detection of a marker produced by the tumor itself
but by the immune system response to the tumor. Specifically the
profile of TCR and/or BCR can provide an insight on whether the
body is mounting a response to a tumor or not. This can ameliorate
some of the issues with current biomarkers. First the immune
response is an amplification signal that can be easier to detect.
Second lymphocytes pass through the blood regularly and hence the
relevant biomarker may readily present and detectable in peripheral
blood than traditional tumor biomarker. Finally the problem of
"background" biomarker material generated by the normal tissue is
greatly reduced. The great diversity of T and/or B cells provide a
way to detect the relevant biomarker with high sensitivity and
specificity, particularly with the recent availability of high
throughput methods for DNA sequencing. The approach of using the
immune system response to cancer to detect it leverages the
foundations laid to this field by the promise of immunotherapy.
However the risk for the two applications is probably quite
different. To use the immune response to cancer for its detection
does not require that the specific clonotype be effective in
treating the tumor but rather that it is associated with the immune
response to the tumor.
Another embodiment of this invention contemplates the combination
of the immune profiling tests with other markers that are already
in use for the detection of cancer to allow tests with greater
sensitivity and specificity. Other molecular identifiers or markers
can be used in computing the Load algorithm or for determining the
disease state. Molecular identifiers can include nucleic acids,
proteins, carbohydrates, and lipids, and expression profiles of
nucleic acids or proteins. The molecular identifiers can be of
human or non-human origin (e.g., bacterial). The identifiers or
markers can be determined by techniques that include, for example,
comparative genomic hybridization (CGH), chromosomal microarray
analysis (CMA), expression profiling, DNA microarray, high-density
oligonucleotide microarray, whole-genome RNA expression array,
peptide microarray, enzyme-linked immunosorbent assay (ELISA),
genome sequencing, copy number (CNV) analysis, small nucleotide
polymorphism (SNP) analysis, immunohistochemistry, in-situ
hybridization, fluorescent in-situ hybridization (FISH), PCR,
Western blotting, Southern blotting, SDS-PAGE, gel electrophoresis,
and Northern blotting.
C. Utility of Immune Profiling in Transplant Medicine
These methods can be used to detect immune rejection of
transplanted organs. Transplantation of organs have become an
integral part of medicine with over 25,000 solid organ (kidney,
liver, heart, pancreas, and lung) transplants and more than 15,000
bone marrow transplants occurring in the US per year. These are
generally complicated procedures done at tertiary care centers. To
minimize the risk of transplant rejection, patients are often
placed on immunosuppression for extended periods of time subjecting
them to the risk of cancer and infections. Furthermore many
transplants are rejected either acutely or years after the
transplantation. In spite of these issues organ transplant remains
an essential treatment modality as patients with organ failures
have few other alternatives.
Solid organ transplant rejection primarily occurs due to response
of the adaptive immune system to the transplanted organ. This is
due to the presence of alloantigens in the graft that are
recognized by the host's immune system, The rejection can occur in
three different phases. The first is the hyperacute phase within
minutes of the transplant where preformed antibodies mount a
response to the graft. The second is the acute rejection that
occurs in first weeks or months after the transplant. The last is
chronic rejection that can occur years after the transplantation.
Given these risks care has been taken to minimize the immunogenic
differences between the donor and recipient. For example the risk
of the hyperacute reaction is greatly reduced when the donor and
recipient are matched for their ABO subtypes as well as tested for
cross matching (determining whether the recipient has antibodies
that react with the leukocytes of the donor). Similarly careful
matching for the Major HistoCompatability (MHC) is done to reduce
acute rejection. However given that MHC molecules are very
polymorphic it is very hard to find to identify a perfect match.
Monozygotic twins have a perfect MHC matching. Similarly 1/4
siblings are expected to have a perfect MHC match. Unrelated
individuals that have the same detected alleles per the clinical
test often have differences due to other polymorphic sites that are
not tested in routine clinical practice. However even with perfect
MHC matching from siblings, there is still a significant risk of
rejection due to the existence of minor histocompatibility
antigens, and indeed acute rejection is very common occurring to
more than half of the grafts.
One might imagine that more aggressive testing of the MHC locus as
well as identification and matching the minor histocompatibility
antigens would significantly improve the graft rejection and
possibly survival rates. While that might be true the limited
numbers of available donor organs available makes this task
impractical as more aggressive testing may significantly delay the
identification of an appropriate graft to be used for each patient.
Therefore, much of the progress that has occurred in the
transplantation field was in the use of immunosuppressive agents to
prevent and treat rejection. Currently many drugs are utilized for
this purpose including: Azathioprine, corticosteroids,
Cyclosporine, Tacrolimus, Mycophenolate Acid, Sirolimus,
Muromonab-CD3, Monoclonal Anti-CD25 Antibody, Monoclonal Anti-CD20
Antibody, and Calcineurin inhibitors.
Bone marrow transplant is most frequently used for leukemia and
lymphoma treatment. Typically the recipient undergoes an aggressive
regimen of radiation and/or chemotherapy to decrease the load of
the tumor before the transplantation. Mature T cells from the donor
can attack some of the host tissues in the inverse rejection that
is called Graft Vs Host Disease (GVHD). This is often manifested by
rash, diarrhea, and liver disease. Careful matching of MHC can
ameliorate but not eliminate this problem. One solution is the
depletion of the donor bone marrow in vitro of mature T cells that
are ultimately responsible for GVHD. One problem with this is that
the same phenomenon that causes GVHD may be responsible for some of
the therapeutic effect of bone marrow transplant through the graft
vs. leukemia effect where donor T cells attack the remaining cancer
cells. In addition depletion of donor T cells can expose to patient
to the risk of being immunodeficient. Therefore the risk and
benefits have to be balanced when considering these approaches.
Patients are therefore often treated with immunosuppressants to
prevent as well as treat GVHD.
Current management of bone marrow but even more so for solid organ
transplantation rely heavily on the treatment with strong
immunosuppressive agents. However given that these drugs have
significant risks they are used in a manner to balance risk and
benefit. However given that the risk for a specific patient at a
particular time is not well understood patients are treated with
the dose where risk and benefits are balanced for the average
patient. Tests that can predict future rejection events may
potentially be very helpful in tailoring treatment to the patients
at the appropriate times they need them. This may result in
reduction in the immunosuppressive doses or some of the patients
while improving the rate of rejection and hopefully graft
survival.
Another embodiment of this invention contemplates the combination
of the immune profiling tests with other markers that are already
in use for the detection of transplant rejection to allow tests
with greater sensitivity and specificity. Other molecular
identifiers or markers can be used in computing the Load algorithm
or for determining the disease state. Molecular identifiers can
include nucleic acids, proteins, carbohydrates, and lipids, and
expression profiles of nucleic acids or proteins. The molecular
identifiers can be of human or non-human origin (e.g., bacterial).
The identifiers or markers can be determined by techniques that
include, for example, comparative genomic hybridization (CGH),
chromosomal microarray analysis (CMA), expression profiling, DNA
microarray, high-density oligonucleotide microarray, whole-genome
RNA expression array, peptide microarray, enzyme-linked
immunosorbent assay (ELISA), genome sequencing, copy number (CNV)
analysis, small nucleotide polymorphism (SNP) analysis,
immunohistochemistry, in-situ hybridization, fluorescent in-situ
hybridization (FISH), PCR, Western blotting, Southern blotting,
SDS-PAGE, gel electrophoresis, and Northern blotting.
D. Utility of Immune Profiling in the Treatment of Infection
These methods have utility in guiding the treatment of infections
particularly when these infections can exist in active and latent
states. The advent of antibiotics for the treatment of infectious
disease over the past century has made a great impact on life
expectancy. Over the past decade molecular diagnostics techniques
have taken a rapidly increasing role in the diagnosis and
management of infectious disease. The excellent sensitivity and
specificity provided by nucleic acid amplification has enabled the
application of these techniques to an increasing number of
applications. Many of the applications are used for the diagnostic
evaluation of the presence or absence of infectious agents. For
example the testing of sexually transmitted diseases is often done
by a molecular testing employing nucleic acid amplification
technique. Another set of application involve the assessment of the
"load" of the infection in a patient with an already diagnosed
infectious agent. An example of that is the assessment of HIV viral
load in patients already diagnosed with AIDS. This test helps the
physician in determining whether the state of the patient's disease
and hence can provide guidance on the effectiveness of the
treatment regimen being used.
It is sometimes helpful not only to consider the level of the
infectious agent but also the immune response to the infectious
agent. One example where the immune response to the infection is
used routinely in clinical practice is in hepatitis B. One aspect
of hepatitis B testing relies on detecting the infectious agent
through detection of hepatitis B antigens of by a nucleic acid
amplification assay. In addition it is common in routine clinical
practice to test for the presence of different antibodies that
target the hepatitis B virus. The presence of anti-HBc IgM usually
occurs in an acute infection setting, the appearance of anti-HBc
IgG indicates the infection is chronic. Similarly the emergence of
anti-HBs antibody signals clearing of the infection.
In one embodiment of this invention the value of the assessing the
immune response to an infection is harnessed along with the
sensitivity and specificity of the molecular testing. This can be
particularly useful for infectious diseases that are chronic where
the infectious agent remains latent in the body. The profile of the
TCR and/or BCR can be used to assess the immune response to an
infection. Sequencing can be used to obtain a profile of the TCR
and/or BCR allowing the detection of particular clonotypes with
high sensitivity and specificity. To determine the specific
clonotypes that correlate with disease several approaches are
conceived.
Another embodiment of this invention contemplates the combination
of the immune profiling tests with other markers that are already
in use for the detection of infectious agents to allow tests with
greater sensitivity and specificity. Other molecular identifiers or
markers can be used in computing the Load algorithm or for
determining the disease state. Molecular identifiers can include
nucleic acids, proteins, carbohydrates, and lipids, and expression
profiles of nucleic acids or proteins. The molecular identifiers
can be of human or non-human origin (e.g., bacterial). The
identifiers or markers can be determined by techniques that
include, for example, comparative genomic hybridization (CGH),
chromosomal microarray analysis (CMA), expression profiling, DNA
microarray, high-density oligonucleotide microarray, whole-genome
RNA expression array, peptide microarray, enzyme-linked
immunosorbent assay (ELISA), genome sequencing, copy number (CNV)
analysis, small nucleotide polymorphism (SNP) analysis,
immunohistochemistry, in-situ hybridization, fluorescent in-situ
hybridization (FISH), PCR, Western blotting, Southern blotting,
SDS-PAGE, gel electrophoresis, and Northern blotting.
E. Utility of Immune Profiling in the Treatment of Aging
Patients
These methods have utility in monitoring the state of the immune
system in the aged. Older people suffer from a decline in the
immune system called immunosenescence that affects their ability to
respond to infections and to raise effective responses to vaccines
(Weinberger et al., 2008). This is apparent from the high mortality
rates due to pneumonia in the elderly (Office for National
Statistics, 2005), and their susceptibility to hospital-acquired
infections, such as Clostridium difficile and methicillin-resistant
Staphylococcus aureus (Health Protection Agency, 2008). Furthermore
the decline in the immune system ability is thought to explain the
increased rate of cancers in the elderly. In addition
immunosenescence may contribute to other major diseases of the
elderly with significant component of inflammatory processes, like
Alzheimer and heart disease. An ability to predict which
individuals are most at risk for these deadly outcomes would be
useful to geriatrics physicians as they make clinical decisions
about vaccination, aggressive treatment of infections and
hospitalization.
Many aspects of the innate and adaptive immune system are altered
in immunosenescence. T cells lose responsiveness, macrophages have
a decreased antigen-presenting capacity and altered cytokine
secretion, natural killer cells have reduced toxicity, follicular
dendritic cells cannot present antigen as efficiently, and
neutrophils lose phagocytic ability. There is smaller pool of naive
T and B cells and an increase in the memory and effector pool
leading to a reduced diversity of T and B cell repertoires leading
to the reduction of the ability of the adaptive immune system to
respond to new antigens. In particular T cell repertoires that are
associated with cytomegalovirus (CMV) are greatly increased and as
much as 45% of the total T cell repertoire may be devoted to it. It
has been noted that these expansions are less pronounced in
centenarians.
Studies have suggested that immune markers can predict survival in
the elderly. The degree of diversity of the B cell repertoire has
been shown to predict survival in the elderly at least in one
population. Even though these global differences in TCR and BCR
diversity were shown to predict clinical outcomes but these markers
lack specificity. Deeper analysis of the repertoire data may
provide significantly more prediction accuracy. For example,
expansions responsive to CMV may have a different significance than
other expansions.
In one embodiment of this invention, RNA from the T and B cells
found in peripheral blood can be collected from a longitudinal
cohort of aging patients whose clinical histories are followed for
several years. The TCR.alpha. and TCR.beta. genes and the IgH, IgK
and IgL genes can be amplified in each of these cohorts at several
time points in their clinical histories. Profiles of patients with
long survival will be compared to patients with short survival.
First, global measure of diversity can be obtained. This will
include not only the number of different clonotypes identified but
also their diversity. For example, is the V, D, J segment usage the
same in the two groups or is one group more restricted in its
usage? For example two samples may have the same number of
independent clonotype but the clonotypes for one of the two samples
do not cover many of the V segments. It is logical to expect that
this sample would be less versatile in responding to a new antigen
compared with the other sample whose clonotypes are distributed
among all the V segments.
In addition to global diversity it will be determined whether
expanded clonotypes in patients who had a long survival can be
distinguished on the basis of some sequence parameter compared to
clonotypes in patients who had a short survival. This approach can
be supplemented by looking at clonotypes that respond to specific
antigens. For example given the available evidence identification
of CMV responsive clonotypes can have predictive power. Capturing T
cells clonotypes that are CMV reactive in a discovery study can be
done from a set of elderly as well as healthy patients. Sequences
of these clonotypes can be studied to identify parameters that
distinguish them from other clonotypes. Using this predictive
algorithm of CMV clonotypes with the longitudinal cohort described
above it can be assessed whether adding this information can add to
the ability to predict the patient who survive for a long time from
that who does not.
Another embodiment of this invention contemplates the combination
of the immune profiling tests with other markers that are already
in use for the detection of health in the aging population to allow
tests with greater sensitivity and specificity. Other molecular
identifiers or markers can be used in computing the Load algorithm
or for determining the disease state. Molecular identifiers can
include nucleic acids, proteins, carbohydrates, and lipids, and
expression profiles of nucleic acids or proteins. The molecular
identifiers can be of human or non-human origin (e.g., bacterial).
The identifiers or markers can be determined by techniques that
include, for example, comparative genomic hybridization (CGH),
chromosomal microarray analysis (CMA), expression profiling, DNA
microarray, high-density oligonucleotide microarray, whole-genome
RNA expression array, peptide microarray, enzyme-linked
immunosorbent assay (ELISA), genome sequencing, copy number (CNV)
analysis, small nucleotide polymorphism (SNP) analysis,
immunohistochemistry, in-situ hybridization, fluorescent in-situ
hybridization (FISH), PCR, Western blotting, Southern blotting,
SDS-PAGE, gel electrophoresis, and Northern blotting.
F. Utility of Immune Profiling in the Administration of
Vaccines
These methods have utility in the administration of vaccines. The
use of vaccination has led to a great reduction in the rate of
infections of multiple organisms. One infectious disease that
continues to have a significant health impact with over 30,000
deaths a year in the US is Influenza. Influenza vaccination has to
be done yearly as the strain mutates rapidly. Most of the severe
sequelae of the disease occur in the elderly. Unfortunately the
elderly often experience immunosenescence rendering them
inadequately responsive to the vaccination.
In order to distinguish patients who are responsive to vaccination
from those that are not, a discovery study needs to be performed.
In this population pre and (at one or more set time) post
vaccination blood samples are available for a cohort of Influenza
vaccinated patients with known Influenza outcome (i.e., were they
later protected from the infection or not). TCR and/or BCR sequence
can be obtained from these samples. Clonotypes that are enriched
after vaccination in each patient are determined. Enriched
clonotypes in patients who responded to the vaccination are then
compared to a control set of clonotypes (e.g., the rest of the
clonotypes in the same set of patients) to distinguish the
correlating clonotypes from other clonotypes. The algorithm to
predict these clonotypes is then used to predict correlating
clonotypes among patients who did not respond to the vaccination.
Patients who did not respond may generate the same type of
clonotypes as those that responded but at lower levels.
Alternatively it might be that non-responders generate a distinct
class of clonotypes. The number of correlating clonotypes
identified in the non-responder may distinguish these two
possibilities.
With the correlating clonotypes identified, an algorithm is then
built to generate a score for predicting likelihood of
immunization. Data from the profiles of the vaccine-responders and
those that do not respond are utilized to generate this algorithm.
This algorithm can then be used to predict the likelihood of
immunization in the next patient using the predicted correlating
clonotypes from a sample obtained after immunization. The
prediction is done through the application of another algorithm
that has also been generated in the discovery study. It can
optionally be aided (or substituted) by data from the
pre-calibration to limit the search for correlating clonotypes to
those that were enriched after immunization.
Another embodiment of this invention contemplates the combination
of the immune profiling tests with other markers that are already
in use for the detection of response to vaccination to allow tests
with greater sensitivity and specificity. Other molecular
identifiers or markers can be used in computing the Load algorithm
or for determining the disease state. Molecular identifiers can
include nucleic acids, proteins, carbohydrates, and lipids, and
expression profiles of nucleic acids or proteins. The molecular
identifiers can be of human or non-human origin (e.g., bacterial).
The identifiers or markers can be determined by techniques that
include, for example, comparative genomic hybridization (CGH),
chromosomal microarray analysis (CMA), expression profiling, DNA
microarray, high-density oligonucleotide microarray, whole-genome
RNA expression array, peptide microarray, enzyme-linked
immunosorbent assay (ELISA), genome sequencing, copy number (CNV)
analysis, small nucleotide polymorphism (SNP) analysis,
immunohistochemistry, in-situ hybridization, fluorescent in-situ
hybridization (FISH), PCR, Western blotting, Southern blotting,
SDS-PAGE, gel electrophoresis, and Northern blotting.
G. Utility of Immune Profiling in the Monitoring of Immune
Hypersensitivity (Allergy)
The adaptive immune system has evolved to respond to antigens that
are associated with pathogens. As is in the case of autoimmune
diseases, the immune system can sometimes have the wrong target.
Whereas in autoimmune diseases the immune system targets self
antigen, in hypersensitivity reactions it mounts a response to
harmless stimuli like medications, dust, and food. Hypersensitivity
is very common with as many as 50% of the US population having
allergy to an environmental stimulus, and it is caused by
mechanisms. Hypersensitivity is divided into 4 types. Type I
hypersensitivity is the immediate type hypersensitivity and is
mediated by IgE. Type II is often due to IgG antibody binding to
cell surface-associated antigen. For example a harmless drug that
binds to the surface of the cell can make the cell a target for
anti-drug IgG in patients who happened to have these antibodies.
Type III is caused by deposition of antigen-antibody complexes on
tissues. This occurs for example when the amount of antigen is
large resulting in small immune complexes that can't be cleared
efficiently and are instead deposited on blood vessel walls. Type
IV sensitivity is a delayed type hypersensitivity mediated by T
cells. Type I and type IV have the highest impact on human
health.
In Type I hypersensitivity reaction the patient becomes sensitized
to a harmless antigen (allergen) by producing IgE antibody against
it. Later exposure to the allergen induces the activation of
IgE-binding cells, such as mast cells and basophils. Once activated
these cells cause the allergic reaction through inducing an
inflammatory process by secreting stored chemicals and synthesizing
cytokines, leukotrienes, and prostaglandins. The dose and the route
of entry of the allergen determines the magnitude of the allergic
reaction that can range from symptoms of allergic rhinitis to the
life-threatening circulatory collapse in anaphylaxis. Often the
acute Type I reaction is later followed by another late phase that
is plays a role in many of the resulting pathological processes.
The late phase of recruitment of T helper cells and other
inflammatory cells is essentially a Type IV hypersensitivity
reaction. Some Type I allergic reactions include seasonal
rhinoconjunctivitis (hayfever), food allergy, drug-induced
anaphylaxis, atopic dermatitis (eczema), and asthma. These are very
common conditions with rising prevalence causing significant costs
as well as morbidity and mortality. For example, Asthma is a
chronic disease that inflicts .about.7% of the US population
causing .about.4,000 deaths a year. Some of these diseases have
some related aspects. For example, patients with atopic dermatitis
are at significantly increased risk to have asthma. Food allergy
can cause vomiting and diarrhea but can also result in anaphylaxis
in a significant number of patients--30,000 cases resulting in
.about.200 deaths per year in the US. Some of the same allergen
that activates submucosal mast cells in the nose causing symptoms
of allergic rhinitis can also activate mast cells in the lower
airways causing bronchial constriction, a typical symptom of
asthma. Some Type IV hypersensitivity reactions are contact
dermatitis (e.g., poison ivy), chronic rhinitis, chronic asthma,
and celiac disease. Celiac disease is a chronic disease caused by a
non-IgE mediated food allergy. It is a disease of the small
intestine caused by the allergic response against gluten, a
component present in wheat and other foods. Over 95% of patients
celiac patients have a specific MHC class II allele, the
HLA-DQ2.
Treatment of hypersensitivity reactions differs, but they often had
two aspects: the acute treatment and chronic management or
prevention. Some of these conditions can be life threatening
(anaphylaxis, and acute asthma) and involve immediate medical
attention. The chronic management in general it involves trying to
avoid the specific allergen. This may be effective when the
allergen can be clearly identified (e.g., allergy to nuts), but
this can be difficult when the allergen is present widely in the
environment, like pollen or dust. Therefore chronic treatment with
medications is often utilized for some of these diseases (e.g.,
asthma and allergic rhinitis). The level of effectiveness of the
treatment management is ultimately tested when the patient is
re-exposed to the allergen(s). Therefore some patients may be
subject to over- or under-treatment. Ideally a test that assesses
the disease activity and the degree to which the patient is prone
to mount a hypersensitivity response would be available. Such a
test would allow the tailoring of treatment to the individual
patient needs.
EXAMPLES
Example 1
Determining the Sequence of Recombined DNA in a Subject with an
Autoimmune Disease
A blood sample is taken from a patient with an autoimmune disease.
CD4+ and CD8+ cells are isolated from the blood sample using
antibody-coated magnetic beads. PCR is used to amplify the full
variable region of the T cell receptor .beta. gene. The amplified
fragments are subcloned into vectors and transformed in bacteria to
isolate the DNA fragments. The bacteria are grown to amplify the
DNA, and dideoxy sequencing is used to sequence the variable
regions of the T cell receptor .beta. gene to identify the
clonotypes. The sequencing information is used to generate a
clonotype profile for the patient. A similar method is shown in
FIG. 1.
Example 2
Determining the State of an Autoimmune Disease
A sample of cerebral spinal fluid (CSF) and blood is taken from a
patient with an episode peak of multiple sclerosis. CD4+ cells are
isolated from the CSF and blood, and the CDR3 of the T cell
receptor .beta. gene is amplified by PCR. The amplified fragments
are subcloned into vectors and transformed in bacteria to isolate
the DNA fragments. The bacteria are grown to amplify the DNA, and
dideoxy sequencing is used to sequence the variable regions of the
T cell receptor .beta. gene to identify the clonotypes. The
sequencing information is used to generate a clonotype profile for
the patient.
Another blood sample is taken when the patient is at a relatively
inactive state of multiple sclerosis. The same procedure as above
is repeated to generate a clonotype profile. Pathological
clonotypes are identified as those that are high at the peak
episode and went down significantly at the inactive state. Another
blood sample is taken from the patient at a later state. At this
time only a fraction of the T cell receptor .beta. gene CDR3
regions are amplified and then sequenced. This subset contains the
pathological clonotypes. The level of the various clonotypes is
determined to assess the disease state of the patient.
Example 3
TCR.beta. Repertoire Analysis: Amplification and Sequencing
Straw
To study amplification of the TCR repertoire, TCR.beta. chains will
be analyzed. The analysis will include amplification, sequencing,
and analyzing the TCR.beta. sequences. One primer
AGCGACCTCGGGTGGGAACA (SEQ ID NO: 135) is complementary to a common
sequence in C.beta.1 and C.beta.2, and there are 34 V primers
(Table 1) capable of amplifying all 48 V segments. C.beta.1 or
C.beta.2 differ from each other at position 10 and 14 from the J/C
junction. The primer for C.beta.1 and C.beta.2 will end at position
16 bp and should have no preference for C.beta.1 or C.beta.2.
The 34 V primers are modified from an original set of primers
published by the BIOMED-2 group in order to amplify all 48 V
segments and all their published alleles as defined by the
international ImMunoGeneTics information system
(http://imgt.cines.fr/).
The BIOMED-2 primers have been used in multiplex in order to
identify clonality in lymphoproliferative diseases.
TABLE-US-00001 TABLE 1 Primer sequences complementary to the
different V families. V segment family Primer sequence SEQ ID NO:
V20-1 AACTATGTTTTGGTATCGTCAGT 1 V29-1 TTCTGGTACCGTCAGCAAC 2 V9,
5-1, 5-6, 5-5, 5-8, 5-4A AGTGTATCCTGGTACCAACAG 3 V9, 5-1, 5-6, 5-5,
5-8, 5-4B AGTGTGTACTGGTACCAACAG 4 V9, 5-1, 5-6, 5-5, 5-8, 5-4C
ACTGTGTCCTGGTACCAACAG 5 V9, 5-1, 5-6, 5-5, 5-8, 5-4D
AGTGTGTCCTGGTACCAACAG 6 V9, 5-1, 5-6, 5-5, 5-8, 5-4E
TCTGTGTACTGGTACCAACAG 7 V7-3, 7-6, 7-9, 7-2, 7-4A
CCCTTTACTGGTACCGACAG 8 V7-3, 7-6, 7-9, 7-2, 7-4B
GCCTTTACTGGTACCGACAG 9 V7-3, 7-6, 7-9, 7-2, 7-4C
CCCTTTACTGGTACCGACAAA 10 V7-8, 16A TTTTGGTACCAACAGGTCC 11 V7-8, 16B
TTTTGGTACCAACAGGCCC 12 V7-7 AACCCTTTATTGGTATCAACAG 13 V4-1, 4-3,
4-2A CGCTATGTATTGGTACAAGCA 14 V4-1, 4-3, 4-2B GGCAATGTATTGGTACAAGCA
15 V12-3, 12-4, 12-5 TTTCTGGTACAGACAGACCATGA 16 V3-1
TACTATGTATTGGTATAAACAGGACTC 17 V25-1 CAAAATGTACTGGTATCAACAA 18 V28,
10-3, 6-2, 6-3, 6-1, 6-6, 24-1A ATGTTCTGGTATCGACAAGACC 19 V28,
10-3, 6-2, 6-3, 6-1, 6-6, 24-1B ATGTACTGGTATCGACAAGACC 20 V6-4,
6-9A TGCCATGTACTGGTATAGACAAG 21 V6-4, 6-9B ATACTTGTCCTGGTATCGACAAG
22 V10-1, 10-2, 6-5, 6-9, 6-8, 27A ATATGTTCTGGTATCGACAAGA 23 V10-1,
10-2, 6-5, 6-9, 6-8, 27B ATATGTCCTGGTATCGACAAGA 24 V10-1, 10-2,
6-5, 6-9, 6-8, 27C ATATGTCCTGGTATCGACAAGA 25 V14
TAATCTTTATTGGTATCGACGTGT 26 V19 GCCATGTACTGGTACCGACA 27 V18
TCATGTTTACTGGTATCGGCAG 28 V30 CAACCTATACTGGTACCGACA 29 V11-1, 11-3,
11-2A CATGCTACCCTTTACTGGTACC 30 V11-1, 11-3, 11-2B
CACAATACCCTTTACTGGTACC 31 V2 ATACTTCTATTGGTACAGACAAATCT 32 V13
CACTGTCTACTGGTACCAGCA 33 V15 CGTCATGTACTGGTACCAGCA 34
The use of the primers for amplification was tested with 34
synthetic sequences. The synthetic sequences contained on one side
the sequence of one of the oligonucleotides and on the other side
the complement of the C primer. In between the two primers was 6 bp
corresponding to the restriction enzyme site Cla I. All the
synthetic sequences were amplified with the appropriate primers,
and it was demonstrated through Cla I digestion that the
amplification products were the result of amplifying the synthetic
sequences and not through formation of primer dimers.
The Illumina Genome Analyzer is the sequencing platform of choice.
In each lane, .about.0.15 million reads can be done. Twelve human
and 96 mouse samples per lane will be run, and sequence tags will
be used to distinguish reads of one sample from those of another. A
two-stage amplification screen can be performed, as illustrated in
FIG. 2. As shown in FIG. 2A, the primary PCR will use on one side a
20 bp primer whose 3' end is 16 bases from the J/C junction and is
perfectly complementary to C.beta.1 and the two alleles of
C.beta.2. In the secondary PCR, on the same side of the template, a
primer is used that has at its 3' end the sequence of the 10 bases
closest to the J/C junction, followed by 17 bp with the sequence of
positions 15-31 from the J/C junction, followed by the P5 sequence.
This primer is referred to as C10-17-P5. P5 plays a role in cluster
formation. When the C10-17-P5 primer anneals to the template
generated from the first PCR, a 4 bp loop (position 11-14) is
created in the template, as the primer hybridizes to the sequence
of the 10 bases closest to the J/C junction and bases at positions
15-31 from the J/C junction. The looping of positions 11-14
eliminates differential amplification of templates carrying
C.beta.1 or C.beta.2. Ultimately, sequencing is done with a primer
complementary to the sequence of the 10 bases closest to the J/C
junction and bases at positions 15-31 from the J/C junction (this
primer will be called C'). C10-17-P5 primer can be HPLC purified in
order to ensure that all the amplified material has intact ends
that can be efficiently utilized in the cluster formation.
In FIG. 2B, the length of the overhang on the V primers is shown to
be 14 bp. The first PCR may be helped with shorter overhang. On the
other hand for the sake of the second PCR, it can be advantageous
to have the overhang in the V primer used in the first PCR as tong
as possible because the second PCR will be priming from this
sequence. A very inefficient priming in the second PCR may cause
limitation in the representation in the final data.
A minimum size of the overhang that supports an efficient second
PCR was investigated. Two series of V primers (for two different V
segments) with overhang sizes from 10 to 30 with 2 bp steps were
made. Using the appropriate synthetic sequences, the first PCR was
performed with each of the primers in the series and gel
electrophoresis was performed to show that all amplified. In order
to measure the efficiency of the second PCR amplification SYBR
green real time PCR was performed using as a template the PCR
products from the different first PCR reactions and as primers
Read2-tag1-P7 and Read2-tag2-P7. A consistent picture emerged using
all 4 series of real time data (2 primary PCRs with two different V
segments and two secondary PCR with different primers containing
two different tags). There was an improvement in efficiency between
overhang sizes 10 and 14 bp. However there was little or no
improvement in efficiency with an overhang over 14 bp. The
efficiency remained high as the overhang became as small as 14 bp
because of the high concentration of primers allowing the 14 bp to
be sufficient priming template at a temperature much higher than
their melting temperature. At the same time the specificity was
maintained because the template was not all the cDNA but rather a
low complexity PCR product where all the molecules had the 14 bp
overhang.
As illustrated in FIG. 2B, the primary PCR will use 34 different V
primers that anneal to the other side of the template and contain a
common 14 bp overhang on the 5' tail. The 14 bp is the partial
sequence of one of the Illumina sequencing primers (termed the Read
2 primer). The second amplification primer on the same side
includes P7 sequence, a tag, and Read 2 primer sequence (this
primer is called Read2_tagX_P7). The P7 sequence is used for
cluster formation. Read 2 and its complement are used for
sequencing the V segment and the tag respectively. A set of 96 of
these primers with tags numbered 1 through 96 were created (see
below). These primers can be HPLC purified in order to ensure that
all the amplified material has intact ends that can be efficiently
utilized in the cluster formation.
As mentioned above, the second stage primer, C-10-17-P5 (FIG. 2A)
has interrupted homology to the template generated in the first
stage PCR. The efficiency of amplification using this primer has
been validated. An alternative primer to C-10-17-P5, termed CsegP5,
has perfect homology to the first stage C primer and a 5' tail
carrying P5. The efficiency of using C-10-17-P5 and CsegP5 in
amplifying first stage PCR templates was compared by performing
real time PCR. In several replicates, it was found that PCR using
the C-10-17-P5 primer had little or no difference in efficiency
compared with PCR using the CsegP5 primer.
The molecule resulting from the 2-stage amplification illustrated
in FIG. 2 will have the structure typically used with the Illumina
sequencer as shown in FIG. 3. Two primers that anneal to the
outmost part of the molecule, Illumina primers P5
(AATGATACGGCGACCACCGAG (SEQ ID NO: 35)) and P7
(CAAGCAGAAGACGGCATACGAGAT (SEQ ID NO: 36)) will be used for solid
phase amplification of the molecule (cluster formation). Three
sequence reads are done per molecule. The first read of 100 bp is
done with the C' primer, which has a melting temperature that is
appropriate for the Illumina sequencing process. The second read is
6 bp long only and will be solely for the purpose of identifying
the sample tag. It is generated using the Illumina Tag primer
(AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC (SEQ ID NO: 37)). The final
read is the Read 2 primer, an Illumina primer with the sequence
GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT (SEQ ID NO: 38). Using this
primer, a 100 bp read in the V segment will be generated starting
with the 1st PCR V primer sequence.
A set of 6 bp sequence tags to distinguish different samples run in
the same sequencing lane was designed, where each tag is different
from all the other tags in the set by at least 2 differences. The 2
differences prevent misassignment of a read to the wrong sample if
there is a sequencing error. The alignment done to compare the tags
allowed gaps and hence one deletion or insertion error by
sequencing will also not assign the read to the wrong sample.
Additional features in selecting the tags was to limit single base
runs (4 A or T and 3 G or C) as well as no similarity to the
Illumina primers. In total 143 tags were generated with the premise
that 96 of them will be used.
Real time PCR has been performed with all 34 different primers
using cDNA obtained from a blood sample. Different Ct values were
obtained for the different primers. Each of the PCR products were
run by gel electrophoresis and demonstrated a single band. In
addition all 34 primers were pooled and a PCR was performed and
again a single PCR band was obtained.
Amplification Optimization
The multiplex amplification can use all the V segments. One issue
in amplification of different sequences is the relative
amplification efficiency of the different sequences and the
preservation of the initial relative quantity of the different
sequences in the final amplified material. The relative
amplification efficiency can be subdivided into different
efficiencies of the distinct primer sequences as well as the
different efficiencies of amplification of different sequences
using the same primer. Efficiency difference can be due to distinct
primer sequences. The reaction will be optimized to attempt to get
amplification that maintains the relative abundance of the
sequences amplified by different V segment primers. Some of the
primers are related, and hence many of the primers may "cross
talk," amplifying templates that are not perfectly matched with it.
The conditions can be optimized so that each template can be
amplified in a similar fashion irrespective of which primer
amplified it. In other words if there are two templates, then after
1,000 fold amplification both templates can be amplified
approximately 1,000 fold, and it does not matter that for one of
the templates half of the amplified products carried a different
primer because of the cross talk. In subsequent analysis of the
sequencing data the primer sequence will be eliminated from the
analysis, and hence it does not matter what primer is used in the
amplification as long as the templates are amplified equally.
Since the amount of each template is not known in cDNA, set of
standards have been generated using the 34 singleplex PCR reaction
from cDNA. The product in each of these reactions comprised a
plurality of sequences with one V primer. The different products
were carefully quantitated to create a set of standards at the same
concentration. A pool of all 34 primers was used and 34 real time
PCR were performed using the pool of primers and each of the
standard sequences as a template. Ideally all the 34 standards will
show equal efficiency of amplification by real time PCR. That
suggests that each sequence is amplified equally even though the
presence of cross talk makes it unclear what primers are carrying
out the amplification. This optimization is consistent with the
goal of having equal amplification irrespective of the actual
primers that is incorporated in the amplification product.
Increasing the total primer pool concentration significantly
reduced the dynamic range as expected from increasing the
efficiency of the amplification. Furthermore for templates that
seemed to amplify more efficiently than the average, the
concentration of their perfectly matched primer in the pool was
decreased. Conversely for templates that were inefficiently
amplified the concentration of their perfectly matched primer was
increased. This optimization demonstrated that all the templates
are amplified within 2 fold of the average amplification.
Ideally the primary PCR will have a small number of cycles to
minimize the differential amplification by the different primers.
The secondary amplification is done with one pair of primers and
hence the issue of differential amplification is minimal. One
percent of the primary PCR is taken directly to the secondary PCR.
Thirty-five cycles (equivalent to .about.28 cycles without the 100
fold dilution step) used between the two amplifications were
sufficient to show a robust amplification irrespective of whether
the breakdown of cycles were: one cycle primary and 34 secondary or
25 primary and 10 secondary. Even though ideally doing only 1 cycle
in the primary PCR may decrease the amplification bias, there are
other considerations. One aspect of this is representation. This
plays a role when the starting input amount is not in excess to the
number of reads ultimately obtained. For example, if 1,000,000
reads are obtained and starting with 1,000,000 input molecules then
taking only representation from 100,000 molecules to the secondary
amplification would degrade the precision of estimating the
relative abundance of the different species in the original sample.
The 100 fold dilution between the 2 steps means that the
representation will be reduced unless the primary PCR amplification
generated significantly more than 100 molecules. This translate to
a minimum 8 cycles (256 fold), but more comfortably 10 cycle (1,000
fold). The alternative to that is to take more than 1% of the
primary PCR into the secondary but because of the high
concentration of primer used in the primary PCR, a big dilution
factor is can be used to ensure these primers do not interfere in
the amplification and worsen the amplification bias between
sequences. Another alternative is to add a purification or
enzymatic step to eliminate the primers from the primary PCR to
allow a smaller dilution of it. In this example, the primary PCR
was 10 cycles and the second 25 cycles.
Testing High Fidelity Enzymes
Enzymes with higher fidelity can be used to minimize errors. The
assay has been optimized using Taq polymerase. In order to validate
the use of Accuprime as well as Taq high fidelity a cDNA with the
pool of primers was amplified using Taq polymerase, Accuprime, or
Taq high fidelity. Each of the amplified material was then used as
a template for 34 real time PCR for with each of the 34 V primers
and the 1 C primer. The relative amount of the templates was
quantitated. A high correlation (r.sup.2>0.95) between the
concentration of each template in the Accuprime, Taq high fidelity
and Taq was found, validating the use of these high fidelity
enzymes.
Validation of Amplification Conditions
The optimization was done using a pool of primers on the standard
template not with the cDNA background. The goal was to obtain
validation for these results in cDNA mixture. In order to show
reproducibility, pool of oligos to amplify cDNA in duplicates were
used. Each of the 34 products were quantitated in each of the two
amplifications. As shown in FIG. 5, the reproducibility was
excellent.
For FIG. 5, two primary PCR reactions were performed using the
pooled TCR.beta. primers and the C primer and one cDNA sample as a
template. The relative abundance in each of the amplified material
of template that is amplifiable with each of the 34 V primers (and
the one C primer) was assessed using real time PCR. Using each of
the two amplified products as a template, thirty four different
real time PCR reactions were performed using the C primer and one
of the V primers in each reaction. The relative abundance
determined by real time PCR was highly reproducible using all the V
primers between for the two samples, indicating that the
multiplexed amplification is highly reproducible. The cycle number
(Ct value) for each of the real time PCR amplifications using the
one multiplexed amplification product as a template is shown on the
X axis and using the second multiplexed amplification product as a
template is depicted on the Y axis.
In order to assess the amplification bias a similar technique can
be employed. The pool of oligos can be used to amplify using cDNA
as a template. Then the amount of template amplified by each of the
34 different primers (along with C segment primer) a can be
quantitated using real time PCR and that amount can be compared
with the amount amplified using the same primer from the cDNA.
However, since there is cross talk even if the relative abundance
among the internal sequences in the amplified product and the cDNA
were the same, big differences using this readout may be detected.
To alleviate this issue 12 oligos were designed that can when used
with C segment primer amplify sequences internal to the V segment
primers. If optimization was done appropriately, then the
concentration of these internal sequences should change little
between the cDNA and the amplified products. This is shown is FIG.
6.
For FIG. 6, a cDNA sample was used as a template for a multiplexed
amplification using the pooled TCR.beta. primers and the C primer.
The C primer and primers were used that are downstream (to be named
internal primers) of the V primers used for the initial
amplification and the material from the multiplex amplification
material as a template to assess the relative abundance of the
different sequences. Similarly real time PCR was used to assess the
relative abundance of these same sequences in the cDNA. If the
multiplexed amplification had great bias, the relative abundance in
the amplified material can be very different from that in the cDNA.
As can be seen in FIG. 6, high correlation was seen demonstrating
minimal amplification bias in the multiplexed amplification. The
cycle number (Ct value) for each of the real time PCR amplification
using internal primers, and cDNA and the multiplexed amplification
product as template is shown on X and Y axis, respectively.
Sequencing TCR.beta.
Six multiplexed amplifications with the pooled oligos and one cDNA
sample as a template were used. Three of each of the amplifications
were done with Accuprime and another 3 with high fidelity Taq. Two
amplifications with each enzyme used cDNA that correspond to 500 ng
initial RNA, and one amplification with each enzyme used 10 times
less cDNA. For each of the six reactions a primary and secondary
PCR was performed and the amplified material was sequenced using
the Illumina platform and the scheme described above. 100 bp
sequence from each side was obtained. The primary analysis of the
data was done using the same concepts described below.
To assess reproducibility of the assay it was determined whether
clonotype levels are consistent in the duplicate experiments. As
shown in FIGS. 8A-C, high correlation is obtained when the same
enzyme and starting input cDNA amount was used (each of the 2
comparisons had r.sup.2=0.944). When different enzymes were used
the correlation gets worse (median correlation for the 4 possible
combinations r.sup.2=0.931), and it is only modestly reduced
(r.sup.2=0.924) when the 2 enzymes were used to amplify smaller
input cDNA (corresponding to only 50 ng RNA).
For FIG. 8, identical sequences in each sample were identified.
Then to deal with sequencing errors some clonotypes were coalesced
to form larger clonotypes using the general approaches described in
the section of primary analysis of sequence. The counts of
clonotypes were then computed in each sample. A fraction of the
clonotypes (not shown in the figure) were present in one sample but
not another, likely due to the algorithm coalescing them with
another clonotype in one sample but not the other. The frequency of
clonotypes in a sample is then computed as its number of counts
divided by the total number of reads obtained for that sample. For
example if 1,000 counts are observed for a clonotype in a sample
with 1,000,000 reads, its frequency is computed as 0.1%. FIG. 8A
shows the log.sub.10 of the frequency of each clonotype in the two
duplicate samples using Accuprime and cDNA corresponding to 500 ng
of RNA as input template. The correlation (r.sup.2) between these
duplicates is 0.944. FIG. 8B depicts the log.sub.10 of the
frequency of each clonotype using cDNA corresponding to 500 ng of
RNA as input template and Accuprime (X axis) or High fidelity Taq
(Y axis). There are 4 comparisons with this combination with a
median correlation r.sup.2=0.931. The one shown in the figure has
r.sup.2=0.929. FIG. 8C shows the log.sub.10 of the frequency of
each clonotype using cDNA corresponding to 50 ng of RNA as input
template and Accuprime (X axis) or High fidelity Taq (Y axis). The
observed correlation r.sup.2=0.924.
These results validate the reproducibility of the assay, and
conform to the expectation that reproducibility gets worse when
different enzymes are compared. Further reduction is seen when
lower amount of input cDNA is used reflecting that lower
representation in the input material leads to poorer precision in
reflecting the relative abundance of the different clonotypes in
the blood. Additionally it is possible some of the reduction in the
correlation is due to the additional amplification (10 fold) needed
for the lower input, but this is likely to be the minor effect
given the evidence for the high reproducibility of the
amplification.
Example 4
IgH Repertoire Analysis
Amplification and Sequencing Strategy
One difference between amplification of CDR3 in TCR.beta. and IgH
is that multiple primers for each V sequence will be used in
investigation of IgH due to the possibility of somatic mutations in
IgH. Three different primers for each V segment will be used. The
primers are in regions avoiding the CDRs, which have the highest
somatic mutations. Three different amplification reactions will be
performed. In each reaction, each of the V segments will be
amplified by one of the three primers and all will use the same C
segment primers. The primers in each reaction will be approximately
the same distance from the V-D joint. Assuming the last position of
the V segment as 0, then the first set of primers (A) have the 3'
end at approximately -255, the second (B) have the 3' end at
approximately -160, and the third (C) have the 3' end at
approximately -30. Given the homology between several V segments,
to amplify all the 48V segments and the many known alleles (as
defined by the international ImMunoGeneTics information system
http://imgt.cines.fr/) 23, 33, and 32 primers in the A, B, and C
frames respectively, will be needed. The list of primers are shown
in Tables 2, 3, and 4.
TABLE-US-00002 TABLE 2 Frame A primers Sequence frame A SEQ ID NO:
IGHV1_1 CCTCAGTGAAGGTCTCCTGCAAGG 39 IGHV1_2
CCTCGGTGAAGGTCTCCTGCAAGG 40 IGHV1_3 CCTCAGTGAAGGTCTCCTGCAAGG 41
IGHV1_4 GGGCTACAGTGAAAATCTCCTGCAAGG 42 IGHV2_1
AAACCCACACAGACCCTCACGCTGAC 43 IGHV2_2 AAACCCACAGAGACCCTCACGCTGAC 44
IGHV2_3 AAACCCACACAGACCCTCACACTGAC 45 IGHV3_1
CTGGGGGGTCCCTGAGACTCTCCTG 46 IGHV3_2 CTGGGGGGTCCCTTAGACTCTCCTG 47
IGHV3_3 CAGGGCGGTCCCTGAGACTCTCCTG 48 IGHV3_4
CAGGGCCGTCCCTGAGACTCTCCTG 49 IGHV3_5 CTGGGGGGTCCCTGAAACTCTCCTG 50
IGHV3_6 CTGGCAGGTCCCTGAGACTCTCCTG 51 IGHV3_7
CTGGAGGGTCCCTGAGACTCTCCTG 52 IGHV3_8 CTGGGAGGTCCCTGAGACTCTCCTG 53
IGHV3_9 TGGGGGGGCCCTGAGACTCTCCT 54 IGHV4_1
CTTCGGAGACCCTGTCCCTCACCTG 55 IGHV4_2 CTTCGGACACCCTGTCCCTCACCTG 56
IGHV4_3 CTTCACAGACCCTGTCCCTCACCTG 57 IGHV4_4
CTTCGGAGACCCCGTCCCTCACCTG 58 IGHV4_5 CGGGGACCCTGTCCCTCACCTG 59
IGHV5_1 GATCTCCTGTAAGGGTTCTGGATACAGCT 60 IGHV6
TCGCAGACCCTCTCACTCACCTGTG 61
TABLE-US-00003 TABLE 3 Primers for frame B Sequence frame B SEQ ID
NO: IGHV6 TGGATCAGGCAGTCCCCATCGAGAG 62 IGHV5_1 GCTGGGTGCGCCAGATGCCC
63 IGHV2_1 TGGATCCGTCAGCCCCCAGG 64 IGHV2_2 TGGATCCGTCAGCCCCCGGG 65
IGHV1_1 GTGCGACAGGCCCCCAGACAA 66 IGHV1_2 GGGTGCGACAGGCCACTGGACAA 67
IGHV1_3 GTGCGCCAGGCCCCCGGACAA 68 IGNV1_4 GGGTGCGACAGGCTCGTGGACAA 69
IGHV1_5 GGGTGCAACAGGCCCCTGGAAAA 70 IGHV1_6 GGGTGCGACAGGCTCCTGGAAAA
71 IGHV1_7 GTGCGACAGGCCCCCGGACAA 72 IGHV1_8 GTGCGACAGGCCCCCAGACAA
73 IGHV4_1 TCCGCCAGCCCCCAGGGAAGG 74 IGHV4_2 TCCGGCAGCCCCCAGGGAAGG
75 IGHV4_3 TCCGGCAGCCACCAGGGAAGG 76 IGHV4_4 TCCGCCAGCACCCAGGGAAGG
77 IGHV4_5 TCCGGCAGCCCGCCGGGAA 78 IGHV4_6 TCCGGCAGCCGCCGGGGAA 79
IGHV4_7 TCCGGCAGCCCGCTGGGAAGG 80 IGHV4_8 TCCGCCAGCCCCTAGGGAAGG 81
IGHV3_1 GGTCCGCCAGGCTCCAGGGAA 82 IGHV3_2 GTTCCGCCAGGCTCCAGGGAA 83
IGHV3_3 GGTCCGCCAGGCTTCCGGGAA 84 IGHV3_4 GGTCCGTCAACCTCCGCGGAA 85
IGHV3_5 GATCCGCCAGGCTCCAGGGAA 86 IGHV3_6 GGTCCGCCAAGCTCCAGGGAA 87
IGHV3_7 GGTCCGCCAGGCTCCAGGCAA 88 IGHV3_8 GGTCCGCCAGGCCCCAGGCAA 89
IGHV3_9 GGTCCGCCAGGCTCCGGGCAA 90 IGHV3_10 GGGTCCGTCAAGCTCCAGGGAAGG
91 IGHV3_11 CTGGGTCCGCCAAGCTACAGGAAA 92 IGHV3_12
GGTCCGCCAGCCTCCAGGGAA 93 IGHV3_13 GGTCCGGCAAGCTCCAGGGAA 94
TABLE-US-00004 TABLE 4 Primes for frame C Sequence frame C SEQ ID
NO: IGHV7 CTAAAGGCTGAGGACACTGCCGTGT 95 IGHV6
CTCTGTGACTCCCGAGGACACGGCT 96 IGHV5_1 AGTGGAGCAGCCTGAAGGCCTC 97
IGHV2_1 TGACCAACATGGACCCTGTGGACAC 98 IGHV1_1
ACATGGAGCTGAGCAGCCTGAGATC 99 IGHV1_2 ACATGGAGCTGAGCAGGCTGAGATC 100
IGHV1_3 ACATGGAGCTGAGGAGCCTGAGATC 101 IGHV1_4
ACATGGAGCTGAGGAGCCTAAGATCTGA 102 IGHV4_1 GAGCTCTGTGACCGCCGCGGAC 103
IGHV4_2 GAGCTCTGTGACCGCCGTGGACA 104 IGHV4_3
GAGCTCTGTGACCGCTGCAGACACG 105 IGHV4_4 GAGCTCTGTGACCGCTGCGGACA 106
IGNV4_5 GAGCTCTGTGACTGCCGCAGACACG 107 IGHV4_6
GAGCTCTGTGACTGCAGCAGACACG 108 IGHV4_7 GAGCTCTGTGACTGCCGCGGACA 109
IGHV4_8 GAGCTCTGTGACCGCGGACGCG 110 IGHV4_9 GGCTCTGTGACCGCCGCGGAC
111 IGHV4_10 GAGCTCTGTGACCGCCGCAGACA 112 IGHV4_11
GAGCTCTGTGACCGCTGACACGG 113 IGHV3_1 CAAATGAACAGCCTGAGAGCCGAGGACA
114 IGHV3_2 CAAATGAACAGCCTGAAAACCGAGGACA 115 IGHV3_3
CAAATGAACAGTCTGAAAACCGAGGACA 116 IGHV3_4
CAAATGATCAGCCTGAAAACCGAGGACA 117 IGHV3_5
CAAATGAACAGTCTGAGAACTGAGGACACC 118 IGHV3_6
CAAATCAACAGTCTGAGAGCCGAGGACA 119 IGHV3_7
CAAATGAACAGCCTGAGAGCTGAGGACA 120 IGHV3_8
CAAATGAGCAGCCTGAGAGCTGAGGACA 121 IGHV3_9
CAAATGAACAGCCTGAGAGACGAGGACA 122 IGHV3_10
CAAATGGGCAGCCTGAGAGCTGAGGACA 123 IGHV3_11
CAAATGAACAGCCTGAGAGCCGGGGA 124 IGHV3_12
CAAATGAACAGTCTGAGAGCTGAGGACA 125 IGHV3_13
CAAATGAGCAGTCTGAGAGCTGAGGACA 126
On the C segment side, two sequences with one base difference
between them (GCCAGGGGGAAGACCGATGG (SEQ ID NO: 127), and
GCCAGGGGGAAGACGGATGG (SEQ ID NO: 128)) cover the four segments and
the multiple known alleles of IgG. A scheme similar to the two
stages of PCR for TCR.beta. genes will be used. On the V side, the
same 5' 14 bp overhang on each of the V primers will be used. In
the secondary PCR, the same Read2-tagX-P7 primer on the V side is
employed. On the C side a strategy similar to that used with
TCR.beta. amplification will be used to avoid variants among the
different IgG segments and their known alleles. The primer sequence
(AATGATACGGCGACCACCGAGATCTGGG AAG ACGAT GG GCC CTT GGT GGA (SEQ ID
NO: 129)) comprises the sequence of the C segment from positions
3-19 and 21-28 and it skips position 20 that has a different base
in at least one of the different IgG alleles and the sequence for
P5 that is can be used for formation of the clusters as shown in
FIG. 4.
All the primers in the 3 frames were successful in amplifying a
single band from cDNA. Similarly the primary and secondary PCR
strategy using the three pools of primers in the primary PCR showed
a single band as shown in FIG. 7.
For FIG. 7, multiplexed PCR using 3 pools of primers corresponding
to the 3 frames was done using cDNA as a template. After the
primary and secondary PCR the products were run on an agarose gel.
A denotes the PCR product from the pool of oligos of frame A.
Similarly B and C denote the products of pools B and C. M is a
marker lane. Single bands with the appropriate sizes were obtained
using all 3 pools.
Ultimately, the 3 different reactions from a single sample will
then be mixed at equimolar ratio and subjected to sequencing.
Sequencing will be done from both directions using the two Illumina
primers. 100 bp will be sequenced from each side. The maximal
germline sequences encompassing the D+J segments are .about.30 bp
longer for BCR than TCR. Therefore if the net result of nucleotide
removal and addition at the joints (N and P nucleotides) generate a
similar distribution for IgH and TCR.beta., it is expected that on
average 90 bp and maximally 120 bp of sequence after the C segment
will be sufficient to reach the 3' of the V segment. Therefore, in
most cases, the sequence from the C primer will be sufficient to
reach the V segment. Sequencing from one of the Illumina adapters
should identify the V segment used as well as identify somatic
hypermutations in the V segments. Different pieces of the V
segments will be sequenced depending on which of the three
amplification reactions the sequence originated from. The full
sequence of the BCR can be aligned from different reads that
originated from different amplification reactions. The sequencing
reaction from the one end showing the full CDR3 sequence will
greatly facilitate the accurate alignment of different reads.
Example 5
Primary Analysis of Human Sequence Data
For each patient sample, approximately 1 million high quality reads
of 100 bp paired-end reads each will be obtained. It is assumed
these 1 million reads are independent, originating from 1 million
or more RNA molecules obtained from 1 million cells or more. Reads
with low quality will be eliminated.
An error rate of .about.1% will be anticipated. Error can arise
either from the reverse transcriptase, amplification during PCR or
during sequencing. Error proofing enzymes for the PCR steps will be
used; hence sequencing errors (.about.1%) will be the main source
of error as the PCR error rate is less than 0.1%. The relevance of
PCR and reverse transcriptase error will be greatly magnified in
situations where there is a bottle neck. A bottleneck can occur,
for example, if over 100,000 RNA molecules is started with or one
of the different molecular manipulation steps is inefficient so as
to make the effective population of molecules 100,000. In these
situations the same error that occurred due to PCR or reverse
transcriptase can appear in many clusters.
Data will be obtained for TCR.beta. and IgH. Given the somatic
hypermutation in IgH and the difference in the amplification
strategy, the primary analysis of TCR.beta. and IgH will be
somewhat different.
TCR.beta.
On one end, the C' segment primer for sequencing will be used. The
length of the V segment that will be sequenced will depend on the
length of N+P nucleotides added. Given the average number of added
nucleotides, about 40 nucleotides of the V segment will be
sequenced. On the other end the Illumina sequencing primer P7 will
be used. The sequence of 20 bp of V primer sequence followed by 80
bp of V segment sequence will be obtained.
Reads will be aligned to the germline V segments (including the
different known alleles) to assign a V segment to each read. Reads
that don't substantially match any V segments will be discarded
from further analysis reads. A substantial match will be defined as
one where there is no more than 5 errors. Given a random error rate
of 1% it is expected that this scheme would discard <1% of reads
due to error. The rest of the sequences will be assigned to the V
segment that has the highest match. Primers amplifying V segments
of the same family will often be highly related with one or a few
bases difference between them. These primers can "cross talk",
amplifying other family members. Therefore the beginning of the
sequencing read (the primer) can be for a V segment that is
different from the V segment the rest of the read belongs to. Such
cases will be allowed and do not count as errors.
The sequences from the end of the V segment to the beginning of the
C segment is evaluated. This sequence will be called the DJ region.
This sequence is on average 60 bases with a very small fraction as
large as 90 bases. It is likely to be able to assign the J segment
in most cases as the end close to the C segment is likely to be
preserved. On the other hand, the D segment may be difficult to
assign given its small size (15-16 bp) and the trimming and
addition that occurs on both of its ends. Of note is that when a J
segment is assigned, it is possible to predict the D and C segment.
After assigning the segment, the sequence of the DJ region will be
defined. Error complicates this analysis more than it does for the
C and V segment alignment for two reasons. First error in the DJ
alignment can occur in either of the two reads being aligned
effectively doubling the error rate of alignment of a single read
to the database sequence.
Additionally, one base difference in the C or V alignment can be
readily attributed to error (except for the rare case of a
previously undescribed V germline allele), and sequences having one
base difference to a V segment can be assigned to have the sequence
of the V segment. On the other hand it will not be clear whether a
one base difference between two DJ region reads is due to an error
or a genuine sequence difference between two clonotypes. There are
two possibilities: the reads belong to the same clonotype but have
errors, or there are two or more distinct clonotypes. Clonotypes
will be designated as distinct when the chance of their emergence
by sequencing error is low either because of their frequent
observations or because they diverge in too many bases.
It is expected that PCR error will be concentrated in some bases
that were mutated in the early cycles of PCR. Sequencing error is
expected to be distributed in many bases even though it will be
totally random as the error is likely to have some systematic
biases. It will be assumed that some bases will have sequencing
error at a higher rate, say 5% (5 fold the average). Given these
assumptions, sequencing error becomes the dominant type of error.
Distinguish PCR errors from the occurrence of highly related
clonotypes will play a role in analysis. Given the biological
significance to determining that there are two or more highly
related clonotypes, a conservative approach to making such calls
will be taken. The detection of enough of the minor clonotypes so
as to be sure with high confidence (say 99.9%) that there are more
than one clonotype will be considered. For examples of clonotypes
that are present at 100 copies/1,000,000, the minor variant will be
detected 14 or more times for it to be designated as an independent
clonotype. Similarly, for clonotypes present at 1,000
copies/1,000,000 the minor variant can be detected 74 or more times
to be designated as an independent clonotype. This algorithm can be
enhanced by using the base quality score that will be obtained with
each sequenced base. If the relationship between quality score and
error rate is validated above, then instead of employing the
conservative 5% error rate for all bases, the quality score can be
used to decide the number of reads that need to be present to call
an independent clonotype. The median quality score of the specific
base in all the reads can be used, or more rigorously, the
likelihood of being an error can be computed given the quality
score of the specific base in each read, and then the probabilities
can be combined (assuming independence) to estimate the likely
number of sequencing error for that base. As a result, there will
be different thresholds of rejecting the sequencing error
hypothesis for different bases with different quality scores. For
example for a clonotype present at 1,000 copies/1,000,000 the minor
variant is designated independent when it is detected 22 and 74
times if the probability of error were 0.01 and 0.05,
respectively.
After designating clonotypes that occur too frequently to be due to
error as distinct or independent, criteria will be considered that
allow designation of clonotypes as independent due to their
differences in too many bases. It is expected that less than 0.1%
of time, two reads will have more than 4 errors in 60 bp between
them. Therefore this will be used as a cut off to consider two
clones as independent or distinct. The algorithm that will be
employed will be as follows. The clonotype with the largest number
of counts (clonotype 1) will be noted, and it will be determined
whether there are any other clonotypes that have the same V segment
and have 4 or less base differences from it in the DJ region. If
more than one such clonotype is identified, the largest of these
clonotypes will be assessed first. The rule described above will be
applied to decide whether to designate the clonotype as an
independent clonotype or the same as the major clonotype. If it is
not designated as an independent clonotype it will then be counted
as if it has the sequence of clonotype 1. At the end of this
exercise the sequence and counts for all clonotypes will be
obtained. This approach ensures that clonotypes will not be
designated as independent when they are not. However, some truly
independent clonotypes may be misclassified (not frequent with low
number of differences from the major clonotype) as being the same.
This type of error will be much less damaging than considering two
clonotypes as independent when they are not.
IgH
For sequencing of the C segment end, the Illumina primer will be
used. The first bases to be sequenced will be the C segment primer
followed by 0-2 bases of C segment and then the DJ region. The
primer sequence will identify which isotype the specific read
belongs to. All or most of the DJ sequence can be obtained through
the read from the C segment side. It is expected that the DJ region
will be on average 80 bp. Therefore, 100 bp read will encompass the
C segment primer and the average DJ region. Some DJ regions may be
as large as 120 bp, and their full reading can include sequencing
data from the V region (not counting those cases where 2 D segments
are found in the same IgH).
The sequence of the DJ region obtained from the C segment will
initially be considered. The number of each unique sequence will be
counted. As discussed for TCR.beta., some of the related sequences
originate probably from the same clonotype but have some sequencing
and PCR error. To designate two clonotypes as distinct, it will be
determined whether the difference is very unlikely to have arisen
through PCR error. The same scheme as above of demanding a minimum
number of independent observations of the minor clonotypes or a
minimum number of differences between the two clonotypes will be
used. The same rules described for TCR.beta. to ensure that
<0.1% of clonotypes are misclassified as distinct will be
employed.
Sequencing from the V region will be done using an Illumina primer.
There will be 3 different primers for each V segment. The primers
will be placed at approximately -200, approximately -100, and
approximately -30. The first sequenced bases will be the V primer
sequence followed by more of V segment bases. The specific read to
one of the three priming frames of a specific V segment will be
assigned. The assignment will be first done through investigating
the primer sequence since the primers have a known sequence that
can't change. Primers of the same family can sometimes have some
"cross talk" amplifying highly related sequence in the same family.
The primers will be used to assign the family. The specific V
segment among the segments in the family will be determined by
identifying the V sequence of the family that is most similar to
that of the sequencing read. V segments in IgH can have somatic
mutations in the course of the antibody affinity maturation process
and therefore a higher proportion of differences from the germline
sequences will be allowed than for TCR.beta.. Antibodies with more
than 25 mutations (.about.10%) in the VDJ region have been
observed. A read will be assigned to the framework of the V segment
with the closest sequence as long as it has >85% homology to it.
Related clonotypes will be assessed for being independent using the
same scheme as described above. Specifically for clonotypes to be
considered distinct and due to somatic mutations not error, they
need to be either sufficiently frequent or have ample variation
between them to ensure that less than 0.1% of clonotypes
misclassified as distinct when they are not.
For reads that are determined to have the third framework (closest
to the VD junction), the overlap sequence between the paired end
reads will be determined. Bases not aligned with the V segment will
be aligned to the complement of the first read to determine the
overlap. The primers for the third framework will be .about.30 bp
away from the junction. Therefore, if the V is intact approximately
50 bp of sequence can be used to reach the VD junction (20 bp
primer+30 bp), and 100 bp reads will allow 50 bp to be read after
the junction. This is the minimum expected number of bases that
would be read after the VD junction as the deletion of some bases
in V will allow for a longer read after the junction. Even for the
longest DJ region, it is expected that there will be 10 bp overlap
between the sequences from the paired reads. The longest DJ region
is expected to be 120 bp, and 80 bp of it are expected to be read
from the C segment and 50 bp read from the other direction of the V
region leading 10 bp overlap between the paired reads.
Clonotypes that read the same sequence from the C primer but has
different frameworks of the same V segment become candidates for
consolidation in the same clonotypes. If there is overlap between
the sequences obtained from the different frameworks of the V
segment then the determination of whether the clonotypes are
independent or not is done with the same rules as described
above.
As a result of the above analysis, the number of reads for each
clonotype can be counted. Clonotypes that are from the same family
differing from each other only by somatic mutations are identified.
These somatic mutations can be restricted to sequences in the V
segment read from only 1 framework, more than 1 framework, or in
the DJ region.
Example 6
TCR and IgH Repertoire Analysis in SLE Patient Samples
It will first be tested whether there are clonotypes that correlate
with disease activity in patients. Second, a set of sequence
characteristics and/or cell surface markers that distinguish
clonotypes that correlate with disease from those that do not will
be defined. Third, the degree to which clonotype analysis provides
clinically useful information will be measured, such as the
correlation with short term (e.g., 3 month) outcome.
1. Presence of Clonotypes Correlating with Disease
There will be two main tasks: identifying correlating clonotypes
and measuring disease activity from their level. These tasks can be
done in a clinical setting in two steps for each patient:
1) A Calibration test can be done to determine the identity of the
correlating clonotypes for the specific patient. This can be done
by sequencing IgH and TCR.beta. RNA (or linked TCR.alpha.-TCR.beta.
sequence from a single cell) for each patient at a time of a peak
of an episode, at which time the correlating clonotype level can
reach their highest levels.
2) A Monitoring test can be done to determine the level of the
correlating clonotypes at a time point subsequent to the
calibration test. This can be done by sequencing IgH and TCR.beta.
RNA and determining the level of the specific correlating
clonotypes that had been identified in the calibration sample of
the same patient. The level of the correlating clonotypes is used
to compute the disease activity at these points.
Amplification, sequencing, and primary analysis development as
described above will be used to assess patient samples.
Specifically, a set of systemic lupus erythematosus (SLE) patients
will be assessed that have a one year follow up period and serial
blood samples during this period. These patients were seen By Dr.
Michele Petri at Johns Hopkins Medical School every three months
for one year, and clinical measures of disease activity including
Systemic Lupus Erythematosus Disease Activity Index (SLEDAI),
Physician Global Assessment (PGA), as well as multiple lab tests
including C3 (Complement 3) and anti-ds DNA levels are available
for all visits of all patients. Drugs being administered to the
patients, include prednisone, plaquenil, NSAID, NSAIDType,
acetylsalicylic acid (ASA) dose, plavix, diuretic, ACE-Inhibitors
or angiotensin receptor blockers (ARBs), Ca channel blocker, Triam
and, solumedrol, Patients who had at least at one time during the
follow up a significant change in disease activity as defined by a
3 points change on the SLEDAI or a 1 point change in PGA will be
studied. Overall there are 181 patients (with a total of 815 blood
samples) who fit these criteria. RNA from all these blood samples
will be subjected to multiplex PCR using primers described above to
amplify the sequences that encompass CDR3 in IgH and TCR.beta.. All
the amplified materials will be sequenced (to a million reads) and
the abundance of different clonotypes will be determined.
Using the clinical data, sequencing, characteristics that
distinguish clonotypes whose level correlate with disease activity
from those that do not will be identified. Second, an algorithm to
determine disease activity using the blood IgH and TCR.beta.
profile will be developed.
2. Identification of Characteristics of Correlating Clonotypes
It is anticipated that clonotypes that are relevant to the disease
will be increased at the time of high disease activity. However,
not all enriched clonotypes at a point of high disease activity
necessarily correlate with disease. For example, in a particular
patient there might be 10 enriched clonotypes at the point of high
disease activity, but only 5 correlate with the disease. In order
to identify these relevant clonotypes, a subset of clonotypes that
are clearly correlating with disease and another set that clearly
do not correlate with disease will be studied. Characteristics that
distinguish those two classes of clonotypes will be
investigated.
All patients will have at least one significant change in disease
activity during the one year follow up in this experimental design.
The IgH and TCR clonotypes obtained at the peak of disease activity
in each patient will be analyzed. Sets of correlating and not
correlating clonotypes among those with the highest level
clonotypes will be selected. Hence the first step is to define
clonotypes that are at a high level. The specific criteria to
choose the clonotypes that will enter the analysis will include a
combination of frequency rank of the clonotype and the level of
clonotype (number of clonotype reads per million), as well as
evidence the clonotype does not belong to the distribution of low
frequency clonotypes.
This set of clonotypes from each patient sample, termed High
Prevalent Clonotypes (HPC) will be further analyzed. The
correlation of the level of each of these clonotypes with clinical
measures will be evaluated. The correlation of SLEDAI score with
the clonotype level will be computed. For each patient there will
be 4-5 study points that can be used to assess the correlation of
SLEDAI with the level of each HPC. The distribution of these
obtained correlations will be investigated. It is anticipated that
most of the HPCs will have low correlation with SLEDAI. It will be
investigated whether at the high correlation end there is an excess
to what is expected to be generated randomly. For example with 4
and 5 data points it is expected that .about.2.5% and .about.0.6%
of the correlation levels (r.sup.2) will be >0.9 by chance. A
higher proportions of HPCs with r.sup.2>0.9 indicates the
presence of a clonotypes that correlate with disease. In addition
to comparing the number of correlating clonotypes with random
expectation, a permutation analysis will be performed where the
correlation of SLEDAI scores from one patient and the level of
individual HPCs from another will be calculated. The distribution
of correlations generated from this permutation can be used as the
"background" correlation. (To ensure its validity, it will be
confirmed that there is little correlation between SLEDAI between
different patients). Excess correlation at the high correlation
end, e.g., r.sup.2>0.9 will indicate the presence of clonotypes
that correlate with disease. The highest correlating clonotypes as
the set of correlating clonotypes will be picked. Because the
number of HPCs that has a by chance correlation higher than a set
threshold is known (from calculation using random assumption or
through the permutation analysis described above), the threshold to
define the correlating clonotype can be set in such a way as to
have 10% false discovery rate, i.e. 10% of the correlating
clonotypes set will be correlating by chance. A set of HPCs that
have very little correlation with SLEDAI score will be picked.
Those will serve as the set of non-correlating clonotypes. These 2
sets of clonotypes can be further analyzed to identify
characteristics that may distinguish them. These characteristics
can then be looked for in new samples to identify the clonotypes
likely to be correlating with disease activity in these samples.
The blood levels of these clonotypes can then be followed to
determine disease activity.
One complication arises from the premise that clonotype level may
change before disease activity does. Hence it is possible that by
attempting to study only HPCs that highly correlate with SLEDAI,
clinically useful clonotypes that change earlier than SLEDAI may be
eliminated. Another set of clonotypes will be picked that correlate
with a Modified SLEDAI (MSLEDAI) score. MSLEDAI is the same as
SLEDAI in all the study points except those just before a
significant change. For those data points the MSLEDAI score will be
the average between the SLEDAI score at that point and the next
study point. Clonotypes that change before SLEDAI are likely to
show better correlation to MSLEDAI than SLEDAI. It will be
informative to compute the excess number of HPCs that have high
correlation with MSLEDAI than expected by random or permutation
generated expectations.
Characteristics that distinguish correlating clonotypes from those
that do not correlate will then be identified. The analysis will be
done in the exact manner for those clonotypes that correlate with
SLEDAI or MSLEDAI. In either case the goal would be for these set
of characteristics to correctly recapitulate this classification
enabling the identification of correlating clonotypes in the next
set of samples. It is expected that each patient will have a unique
set of correlating clonotypes, but the training study will be
designed to generate the rules that predict the correlating
clonotypes from a calibration sample (at high disease activity).
Two general types of parameters can be tested: those that are
obtained from the sequencing data itself, and those that can use
extra experimentation. Extra experimentation can include the
assessment of different cells with different cell surface or other
markers. Here are a few types of parameters that will be
investigated:
1) Sequence motif: The motif can be a specific V or J region, a
combination VJ, or short sequences in DJ region that is associated
with a clonotype being correlating.
2) Size of the clonotype.
3) Level: Absolute level (number of reads per million) or rank
level.
4) Similarity to other clonotypes: The presence of other highly
related clonotypes, like those with silent changes (nucleotide
differences that code for same amino acids) or those with
conservative amino acid changes.
5) For the BCRs the level of somatic mutations in the clonotype
and/or the number of distinct clonotypes that differ by somatic
mutations from some germline clonotypes.
Each of these parameters will be individually studied for
association with correlating clonotypes. A threshold of 0.05
(uncorrected for multiple testing) will be set to eliminate factors
that are not likely to contribute to prediction of correlating
clonotypes. Given the multiple parameters, many tests will be
performed to generate multiple positive results by chance. However
the main goal of this step is to filter the parameters to a smaller
set. The set of positive parameters will then be used to create an
algorithm to classify the two sets of clonotypes. A machine
learning algorithm will be employed that uses the different
parameters to classify the two sets of clonotypes. In order to
minimize the risk of overfitting, the cross validation technique
will be used. Using this algorithm each clonotype will get a score
that corresponds to the likelihood it is a correlating clonotype. A
threshold will then be placed to classify clonotypes above it as
correlating and those below it as non-correlating. The accuracy of
the classification can be estimated by the cross validation
technique; for example, the clonotypes are put in equal groups and
the algorithm using all clonotypes except one group. Clonotypes in
the last group (test group) are then classified using the algorithm
that was obtained using the rest of the clonotypes. This is
iterated as many times as the number of groups, and in each
iteration all the groups except one are used for training and one
group is classified. The accuracy of the algorithm can be estimated
from the average accuracy of the different classifications in the
different iterations. It is of note that in all these iterations
the exact algorithm would be slightly different. The accuracy of
classification is then an estimate as it is not on the final
algorithm but rather on a set of related algorithms generated with
training data from all clonotypes except one.
Ultimately, two algorithms will be generated trained on two
different correlating clonotypes sets: one correlating with SLEDAI
and the other correlating with MSLEDAI. Even if the clonotypes in
the training set are different the resulting algorithm may or may
not be very different, depending on whether these clonotypes indeed
come from two distinct populations. The algorithms will be
compared. Additionally these algorithms will be used to identify
correlating clonotypes that were not initially in the training set.
The clonotypes identified in the two algorithms will be compared,
and if the initial clonotypes in the two training sets were from
the same population, the identified clonotypes are likely to be
very similar. Unless the results of the algorithm were quite
similar, both algorithms wilt be carried to identify correlating
clonotypes in order to measure lupus disease activity.
Other experimental approaches can add to the power of sequencing in
identifying clonotypes that correlate with diseases. Correlating
clonotypes may be enriched in cells with some surface or other
markers. For example B cells with high levels of CD27 are known in
active lupus patients, and hence it might be that correlating
clonotypes might be enriched in the CD27 population of cells. If
that is borne out to be true, prediction of correlating clonotypes
can be improved by doing an enrichment for cells with high levels
of CD27. Specifically, a sequencing reaction can be performed on
the IgH sequences from all B cells in the blood sample as well as
from those B cells with high CD27. Correlating clonotypes are
expected to be present at higher frequency in the high CD27
population than in the all blood sample.
3. Using IgH and TCR.beta. Profiles to Determine Lupus Disease
Activity
The section above described clonotype-based analysis to identify
features of correlating clonotypes. In addition, for that analysis
only a fraction of all the HPCs were used to clearly designate
clonotypes as correlating or non-correlating. This section
describes analysis that is at the patient level aiming to compute a
measure of disease activity, to be called AutoImm (AI) score. The
algorithm developed per the above section will be applied to
identify correlating clonotypes among all the HPCs. The level of
these correlating HPCs will be determined. The level of the
correlating clonotypes can be normalized to the total number of TCR
clonotypes as well as to HPCs predicted not to correlate with
disease. The level of these correlating clonotypes at different
time points will be used to compute AI score at these different
points.
In patients with more than one correlating clonotypes; the
information regarding the level of these different clonotypes will
be combined. In addition data from IgH and TCR.beta. clonotypes
will be integrated. Different algorithms for making the combination
will be attempted. For example, the average, median, sum, and
highest correlating clonotype level will be studied. The clonotype
level can be its simple linear read counts, the logarithm of that
or some other conversion. It can potentially be the difference
between correlating and non-correlating clonotypes. Furthermore
methods for weighted average can be utilized. The weighting can be
based on the likelihood of a clonotype to be correlating.
In order to evaluate which of the models is optimal, all the models
will be assessed to identify the one that generates the highest
correlation between the AI score and the SLEDAI score. For this
analysis the correlation of SLEDAI and AI scores is done across all
the data obtained from all the study points from all patients. In
order to estimate and ameliorate the degree of overfitting, the
cross validation technique will be used. The level of correlation
measured reflects the "cross sectional" relationship between the AI
and SLEDAI scores. In addition to SLEDAI, the correlation with
other clinical measures like C3 and anti-ds DNA antibody levels as
well as urine protein/serum creatinine for patients with kidney
manifestation and blood counts for patients with hematological
involvement will be studied. The correlation may be due to the
classification of patients into high and low disease activity, and
is not necessarily a reflection of AI correlating with SLEDAI score
within a patient. To demonstrate that, "longitudinal" assessment
will be done.
4. Longitudinal Analysis
In the longitudinal analysis, two general questions will be
assessed: does AI score at one study point predict disease activity
at the same point, and does AI score at one study point predict
disease activity at a later point, e.g., the next study point 3
months later.
The relationship between AI and SLEDAI scores at the same study
point will be assessed in two ways. First the correlation of the AI
and SLEDAI in each patient will be calculated, and then the average
and median patient correlation level will be computed. If the
correlation seen in cross sectional analysis above is due to
classification of high and low disease activity patients and not
changing disease activity within individual patients, then the
longitudinal correlation in individual patients is likely to be
low. A high median patient correlation level suggests that AI does
reflect the SLEDAI score at an individual patient level. In
addition to the correlation of AI and SLEDAI scores, the
correlation of AI with other relevant measures like C3 and anti-ds
DNA antibody will be assessed as well as urine protein/serum
creatinine for patients with kidney manifestation and blood counts
for patients with hematological involvement.
Another way to demonstrate the ability of AI score to measure
disease activity changes in individual patients is by determining
its accuracy in distinguishing states of high from low disease
activity in the same patients. For each of the 181 patients, the
two study points when the SLEDAI where at the highest (to be called
HDAP for high disease activity point) and lowest levels (to be
called LDAP for low disease activity point) will be selected. The
distribution of the AI of all the HDAPs with that of the AI of all
the LDAPs will be compared, and the p-value that they are different
will be computed. In addition, the frequency that the AI at HDAP is
higher than LDAP in each patient will be assessed. If AI does not
change with disease activity in an individual patient then it is
expected that AI at HDAP is higher than that at LDAP only 50% of
times. Another analysis will be done where the fraction of times
that AI at HDAP is higher than that at LDAP by a meaningful
difference (i.e., above the likely AI variation) is determined. To
measure the fluctuation of AI, all the study points from all the
patients will be used, and the standard deviation (and relative
standard deviation) of AI in the different bins of SLEDAI values
can be computed. This will generate relative standard deviation
across all patients (AI-RSDall) and this value may or may not be
dependent on SLEDAI (i.e. the AI-RSDall may be different at
different SLEDAI values). The proportion of patients where AI at
HDAP is higher than AI at LDAP by a specific number (e.g., 2) of
AI-RSDall can be computed. There can be some systematic bias where
the computed AI in some patients is consistently higher (or lower)
than what is expected from the SLEDA score. Therefore AI-RSDall is
a combination of the intrinsic fluctuation of AI within a patient
as well as the systematic difference of AI for patients with
similar SLEDAI. The intrinsic fluctuation of AI can be computed
within a patient by calculating the standard deviation (and
relative standard deviation) of AI scores among study points with
similar SLEDAI values (<2 points difference) within a patient.
The median among all the patients of the relative standard
deviation can be computed (AI-RSDpt-med). The proportion of
patients where AI at HDAP is higher than AI at LDAP by a specific
number (e.g., 2) of AI-RSDpt-med can then be evaluated.
After demonstration that AI does indeed fluctuate with SLEDAI
within individual patients it will be evaluated whether AI can
predict SLEDAI at the next study point, 3 months later. To assess
that correlation level between the AI score at time 0 and the
SLEDAI score at time+3 months can be quantitated. The correlation
can be computed on a patient level and then the median patient
correlation can be obtained. Another way to demonstrate the ability
of AI to predict near future disease activity is to evaluate the
sensitivity and specificity of AI in predicting disease activity 3
months in the future. Clinically, those patients who are doing well
on their current management can be distinguished from those that do
not. A patient state at a particular time will be classified into
one of two classes: Poor Control (PC) and include patients who in 3
months will have high disease activity (SLEDAI >6 points) and/or
a flare (SLEDAI increase by 3 points), and Good Control (GC) and
include patients who in 3 months will have low or moderate with
disease activity (SLEDAI <6) and/or a significant reduction in
disease activity (SLEDAI decrease by 3 points). The classification
sensitivity can then be evaluated and specificity obtained using
different thresholds of AI. A ROC curve that describes the
performance of AI in predicting the state of the patient (PC or GC)
can be generated 3 months ahead of time. The performance obtained
by this test will be compared with that of standard clinical
measures including SLEDAI, anti-ds DNA and C3 levels.
An analysis to evaluate the ability of AI to predict changes in
SLEDAI scores 3 months later will also conducted. Using data from
all study points of all patients, the relationship between AI and
SLEDAI scores can be plotted to identify the "cross sectional"
correlation level as discussed above. This determines the
relationship between SLEDAI and AI at the same study point. This
relationship will be fit with an equation allowing the prediction
of the SLEDAI score given an AI score (or vice versa). If AI
predicts flares then changes in SLEDAI at some study point I will
be preceded by changes in AI at point 0. Therefore, if a flare
occurs between point 0 and 1, the AI score at point 0 (to be called
AImeas) will be higher than what is expected (to be called AIexp)
given the SLEDAI at study point 0. On the other hand with no change
in disease activity between the study point 0 and study point 1,
the AI score at point 0 will be very similar to what is expected
given the SLEDAI at study point 0. The relative AI change
(Rel-AI-diff) can be computed by dividing the difference of AImeas
and AIexp by AImeas. The sensitivity and specificity of AI in
predicting a significant change in SLEDAI 3 months later can be
evaluated by using different thresholds of Rel-AI-diff. The
thresholds can be bidirectional so if the Rel-AI-diff at a specific
study point is higher than a specific threshold a flare is
predicted, and similarly if it is lower than the negative of the
specific threshold a significant reduction in SLEDAI is expected.
On the other hand when the Rel-AI-diff at a study point is between
the threshold and its negative, no significant changes in disease
activity is expected. A ROC curve showing the trade of sensitivity
and false positives can be generated using many different
thresholds of Rel-AI-diff. Similar ROC curves can be generated
using standard clinical measures including SLEDAI, anti-ds DNA and
C3 levels.
If the fluctuation of AI varies at different SLEDAI values, the
above analysis will be refined. A section above described the
computation of AI-RSDall and AI-RSDpt-med and mentioned evaluating
whether they change at different SLEDAI values. If they do then the
ROC analysis can be done as described above but instead of using
different thresholds of Rel-AI-diff, different thresholds of
AI-RSDall and AI-RSDpt-med will be used. The performance obtained
by the test with that of standard clinical measures including
SLEDAI, anti-ds DNA and C3 levels wilt be compared.
In the above analysis, attempts are made to predict the SLEDAI at
point 1 from the AI score at point 0. It is likely that in addition
to the absolute level at point 0, the change of AI from point -1 to
0 will be informative in predicting SLEDAI at point 1. For example
consider a patient who has at study point -1 an AI score of X-1,
and at point 0 the AI score is increased to a new value X0 that is
appreciably higher than X-1. This patient may have higher
likelihood of a flare at point 1 than a patient whose AI has been
stable at X0 at study points -1 and 0. This concept of AI change or
velocity will be incorporated to generate a Modified AI (MAI)
score. To generate a MAI at point 0 the AI score at point -1 and at
point 0 will be needed, and hence one data point per patient will
not have an MAI associated with it. The specific formula to
incorporate the velocity into AI calculation to obtain MAI will be
optimized. This optimization may be done through maximization of
the correlation of MAI and SLEDAI three months later. The cross
validation design will be used to evaluate and control the degree
of overfitting. Correlation can be done for data points of all
samples, but also can be done at a patient level and the median
correlation among all patients can be assessed. The latter approach
ameliorates the issue of some patients having a systematic bias of
too low or too high AI score. Using MAI, the same type of ROC
analysis that was mentioned for AI can be performed to assess its
ability to predict SLEDAI 3 months later. First, analogously to
what is described for AI, an analysis can be done to show the
ability of MAI at point 0 to distinguish PC and GC states at point
1. Additionally, an analysis similar to what was described for AI
to assess the ability of MAI at point 0 can be performed to predict
significant disease activity change (3 points change on SLEDAI)
between points 0 and 1. For this latter analysis different
thresholds of Rel-AI-diff, AI-RSDall or AI-RSDpt-med can be used.
The performance of MAI will be compared with that of AI to
determine whether the addition of the velocity factor is
useful.
One complication of the described study is that treatment changes
are done for different patient during the follow up period of the
study. This is likely to complicate the prediction of disease
activity. For example, consider two patients with the same AI score
at point 0 and one of those patients had a reduction in medication
at the same time. The likelihood of this patient to have a rise in
disease activity at point 1 is then likely to be higher than for
the patient who did not change medications at point 0. This is
likely to lead to underestimation of the performance of AI. One way
to alleviate that is to eliminate all the points with significant
medication changes from the study. Another is to modify the AI
score to include whether a patient has a medication change and
create a medication-modified AI. So in the example above with the
two patients, the one with the medication change will have a higher
medication-modified AI.
5. Integration with Other Predictive Markers
The predictive ability of the disease activity marker can be
maximized. Therefore the predictive ability of the TCR/BCR
repertoire information integrated with other markers will be
tested. These markers include standard markers used in the clinic
like anti-ds DNA and C3 levels. It will also include other markers
that are published. For example a panel of chemokines has already
been shown to have some predictive ability using the same set of
patients as will be used. Whether this panel will increase the
predictive ability of the TCR and BCR repertoire will be evaluated.
The first step is to integrate the AI score with the additional
measure to generate an Expanded AI (EAI) score. Different ways to
do the integration can be assessed, and this can be optimized
through maximization of the correlation of EAI and SLEDAI three
months later. The cross validation design will be used to evaluate
and control the degree of overfitting. Using EAI the ability to
predict disease activity 3 months later will be assessed by its
ability to distinguish GC from PC and to predict changes in disease
activity. The performance in measuring disease activity and change
in disease activity can be described through ROC analysis as
described above.
6. Validation
The number of variables being tested is high compared with the
number of samples. This can lend itself to overfitting, with
initially promising results not being able to be validated in later
studies. A cross validation approach will be used in the training
to get a measure of the extent of overfitting. However, a
validation on an independent set of samples will be involved in
later work. This is not part of this proposal, but this marker can
be clinically applicable. Using the data obtained above, it can be
determined whether AI, MAI, or EAI, should be validated and the
specific way to compute the measure of interest. One specific
algorithm will be taken for validation. In addition one or more
specific endpoints will be specified. The sensitivity and
specificity of AI can be assessed in the ability to distinguish GC
from PC 3 months later to evaluate the ability of AI to predict
disease activity. In another example the sensitivity and
specificity of AI to predict significant disease activity change in
3 month using a specific Rel-AI-diff threshold can be assessed.
Example 7
Measuring Response of an SLE Patient to Drug Therapy
The methods of the provided invention will be used to measure the
response of an SLE patient to drug therapy. Determination of
whether an SLE patient being given an expensive drug with serious
side effects is responding to the drug plays a role in both patient
care and also for making the administration of such care cost
effective. Many clinical indicators of disease activity respond to
treatment imprecisely and after a time lag of up to several months.
During this time, disease may progress and side effects may add
complications to therapy. A prompt understanding of the drug
response would allow patients to be switched to more effective
therapies more rapidly.
In this Example, a 35 year old African American female with a prior
diagnosis of lupus presents to her regular rheumatologist. The
patient's disease status is assessed on a quarterly basis through a
comprehensive clinical assessment in addition to laboratory testing
including measurement of C3, anti-ds DNA antibody levels, blood
counts, and urinalysis. During one visit the patient complains of
skin lesions and fatigue, and urinalysis shows evidence of
proteinuria and/or cell casts. The rheumatologist refers the
patient to a nephrologist for a kidney biopsy to assess
inflammatory status of the kidney and orders serum creatinine and
24 hour urine protein to creatinine ratio to assess the degree of
the impairment of the kidney function. A kidney biopsy shows
evidence of diffuse lupus nephritis, while the urine protein to
creatinine test reveals evidence of nephrotic syndrome (urine
protein to creatinine ratio of 3.6). Based on this information a
diagnosis of acute lupus nephritis is given and the patient is
begun on a course of drug therapy. There are several possible drugs
that can be chosen at this point. Immunomodulators such as
mycophenolate mofetil (Cellcept) are often used although sometimes
in severe cases drugs such as Methotrexate, Azathiopurine (Imuran)
Cyclophosphamide (cytoxan), are prescribed. Rituximab (Rituxan) is
also sometime used as a second or third choice. One of these drugs
is often used in combination with a systemic steroid such as
Prednisone or methylprednisolone in order to suppress the acute
symptoms. Here, mycophenolate mofetil is prescribed at 150 mg per
day alongside 60 mg of prednisone. Given the many side effects of
steroids, including the risk of osteoporosis, hyperglycemia, weight
gain, and other Cushingoid symptoms in the long term, the patient's
prednisone dose is tapered over .about.6 weeks if the clinical
picture allows that.
The first question that is determined is whether the patient is
responding to therapy, and as a result, can the dose of steroid can
be appropriately decreased. Therefore, during this period the
patient's serum creatinine as well as urine protein and creatinine
are followed to ensure the patient is responding to the
medications. Frequent kidney biopsy can be done to detect whether
the inflammatory damage is being reversed; however, routine use of
kidney biopsy carries too great a risk and is too invasive to be
practical. Current blood based markers that are being used to
assess inflammatory status are of limited use in making this
decision in that they are not sufficiently well correlated with
underlying disease to be relied upon to risk the increased side
effects that accompany high doses of steroids. Serum and urine
function markers may have some delay in detecting improvement in
inflammatory status and hence steroids may be tapered before these
markers show a definitive change and hence extending the period of
the renal flare. A slower taper, informed by more sensitive
markers, in these cases could have shortened the flare period
preventing further damage to kidney tissue. After the reduction of
steroid to a maintenance dose of approximately 10 mg the patient
may show persistently elevated levels of protein in the urine and
the high urine protein to creatinine ratio of 2, and the physician
must now decide whether to switch from Cellcept to another
medication. Arguing in favor of this is the continued evidence of
loss of kidney function but without an accurate measure of
inflammatory kidney status, it can be difficult to know whether the
disease itself is in remission having nevertheless done some level
of irreversible kidney damage that is resulting in these persistent
levels of proteinuria. Here again the existing blood based markers
are imperfectly informative and a further kidney biopsies are not
practical. This decision would be greatly aided by an accurate
blood based measure of disease status.
AutoImm Load would be very helpful in this situation to assess the
response to therapy by measuring disease activity either alone or
in combination with other markers of disease activity. An algorithm
for AutoImm Load will be developed using the study described above.
The correlating clonotypes that will be used to calculate AutoImm
Load will be measured using a calibration test. This calibration
test will be done using blood from a patient at a time of peak
disease activity, for example at the start of therapy. The
calibration test will be performed using blood or alternatively
using the tissue that is affected (e.g. kidney biopsy or skin
biopsy). At a later time at which the response to therapy is to be
assessed, a blood sample will be taken and used along with the
calibration test to measure AutoImm Load. This will be used to make
a treatment decision. If the correlating clonotypes are derived
from a populations study, there is no need for the calibration test
and a blood test at the time at which the response to therapy is to
be assessed is sufficient to measure AutoImm Load in order to
inform the treatment decision.
Example 8
Determination of Appropriate Time to Taper or Stop Therapy for an
SLE Patient
The methods of the provided invention can be used to determine the
appropriate time to taper or stop therapy for an SLE patient. In
addition to the time lag that can be exhibited by the clinical
measures of disease activity, a further difficulty lies in the lack
of sensitivity of these measurements. Subclinical disease can
nonetheless result in a re-flaring of the disease if therapy is
tapered too early. As a result of this, courses of
immunosuppressant therapy are typically administered for a time
period that is much longer than is necessary for the average
patient to ensure that the risk of re-flaring is low for the
average patient yet may still be long enough for the tail end of
distribution. Therefore significant over-treatment, causing side
effects and costs are occurring in most patients, while
under-treatment of some patients occurs causing potentially
preventable re-flares. A method that could measure subclinical
activity that was predictive of the risk of re-flaring would allow
therapy to be tapered based on such measures instead of relying on
overtreatment by design.
In this example, the patient from Example 7 is on prednisone and
mycophenolate mofetil for a period of 6 months and urine protein to
creatinine ratio returns to a level of 0.5. This level remains
above the baseline level expected in healthy individuals but it is
not clear that this level is not due to some kidney damage that is
not reversible. Other clinical measures of inflammation are normal
and the patient does not report any other symptoms. At the same
time the patient is experiencing moderate levels of nausea and
weight gain as possible side effects to the medications that
additionally have serious long term side effects. The doctor is
faced with a difficult decision: balancing the fear of tapering the
Cellcept and/or steroid too quickly, which could result in renewed
kidney inflammation and likely further long term irreversible
kidney damage and the adverse reactions that can occur due to the
medications. Here again an unambiguous assessment of the disease
status without having to perform a kidney biopsy would play a role
in making this decision. Attempt of reducing steroids is
recommended through repeated trials of steroids leading to the
recurrence of the same clinical dilemma. In fact this question
arises at every time the patient is in remission and the patient is
on steroids or immunomodulators.
AutoImm Load would be very helpful in this situation to assess
whether or not to taper therapy by measuring disease activity
either alone or in combination with other markers of disease
activity. An algorithm for AutoImm Load will be developed using the
study described above. The correlating clonotypes that will be used
to calculate AutoImm Load will be measured using a calibration
test. This calibration test will be done using blood from a patient
at a time of peak disease activity, for example at the start of
therapy. The calibration test could be performed using blood or
alternatively using the tissue that is affected (e.g. kidney biopsy
or skin biopsy). At a later time at which the level of disease
activity is to be assessed, a blood sample can be taken and used
along with the calibration test to measure AutoImm Load. This will
be used to make a treatment decision and to evaluate whether the
patient has any detectable disease activity. If the correlating
clonotypes are derived from a populations study, there is no need
for the calibration test and a blood test at the time at which the
response to therapy is to be assessed is sufficient to measure
AutoImm Load in order to inform the treatment decision.
Example 9
Prediction of Flares in an SLE Patient
One challenge in treating SLE patients is that represented by the
fact that flares arise without warning, thus thwarting the
physicians' efforts to treat the disease preventively. Waiting for
flares to occur before beginning treatment subjects patients to
potentially destructive clinical symptoms, can involve expensive
and inconvenient hospitalization, and may cause long term organ
damage to be done while also necessitating aggressive therapeutic
interventions that are themselves fraught with side effects. A much
more desirable paradigm would be a therapeutic paradigm in which
flares are detected at a subclinical phase at which time therapy
could be administered proactively saving significant suffering to
the patient, resulting in less expensive hospitalizations and
ultimately enabling better long term prognosis for the
patients.
The patient from Example 7 is recovering from the acute flare
described above, and the patient is tapered off of all therapies
except Plaquinil and a low dose of 5 mg of Prednisone. Nevertheless
this patient remains at a high risk of having another inflammatory
episode. As a result, this patient will remain in the care of a
rheumatologist who will continue following patient's clinical
symptoms and laboratory tests. Unfortunately these symptoms and
tests do not provide early warning for an imminent flare until
patients actually have exhibited clinical symptoms of a flare and
the sequence repeats itself. A highly specific marker of increasing
subclinical activity could be included in the routine clinical
assessment of the patient in order to detect unambiguous signs of a
flare which may reach a clinically detectable stage within the
subsequent 1-3 months. Beginning therapies earlier might make the
flare less severe and may allow treatment to be accomplished with
less long term organ damage or less steroids used than what is
currently the case.
AutoImm Load would be very helpful in this situation to assess the
likelihood of an incipient flare by measuring disease activity
either alone or in combination with other markers of disease
activity. This score either by itself or the rate of increase
(velocity) or acceleration of this score can be used to assess the
likelihood of progression to a flare. An algorithm for AutoImm Load
could be developed using the study described above. The correlating
clonotypes that will be used to calculate AutoImm Load could be
measured using a calibration test. This calibration test could be
done using blood from a patient at a time of peak disease activity,
for example at the start of therapy. The calibration test could be
performed using blood or alternatively using the tissue that is
affected (e.g. kidney biopsy or skin biopsy). At a later time at
which the response to therapy is to be assessed, a blood sample can
be taken and used along with the calibration test to measure
AutoImm Load. This can be used to make a treatment decision. If the
correlating clonotypes are derived from a populations study, there
is no need for the calibration test and a blood test at the time at
which the flare risk is to be assessed is sufficient to measure
AutoImm Load in order to inform the treatment decision.
Example 10
Objective Measure to Assess Subjective Symptoms of SLE Patients
SLE affects many organs and produces many potential symptoms
including ones that are very common in the healthy populations. For
example, if an SLE patient complains of a headache, the headache
may be a sign of CNS lupus or can be due to the common headache.
Similarly, if SLE patients complain of worsening fatigue over a
period of time, the worsening fatigue may be due to deterioration
of their disease or can be due to depression or other causes. The
availability of an objective measure that reflects disease activity
can be of great help in the management of SLE patients.
The patient in Example 7 presents to the rheumatologist with chief
complaints of headache, fatigue, and difficulty with concentration.
Patient's headache is recurrent and only transiently gets better
with Motrin treatment. The patient's SLE is otherwise in good
control. Relevant psychosocial stressors in the patient's life
include that she is going through divorce. Physicians are in a
dilemma when they face SLE patients with symptoms that are
non-specific to SLE and are common in the general population. Is
the patient suffering from CNS lupus? Or could she suffering from
other common causes of her symptoms, like depression? Current
laboratory tests currently lack the sensitivity and specificity to
be relied on to distinguish these possibilities. A reliable test to
measure SLE disease activity can be utilized routinely to help in
distinguishing the two possibilities.
AutoImm Load would be very helpful in this situation to objectively
assess the disease activity either alone or in combination with
other markers of disease activity. An algorithm for AutoImm Load
will be developed using the study described above. The correlating
clonotypes that will be used to calculate AutoImm Load will be
measured using a calibration test. This calibration test will be
done using blood from a patient at a time of peak disease activity,
for example at the start of therapy. The calibration test will be
performed using blood or alternatively using the tissue that is
affected (e.g. kidney biopsy or skin biopsy). At a later time at
which the objective disease activity is to be assessed, a blood
sample can be taken and used along with the calibration test to
measure AutoImm Load. This will be used to make a treatment
decision. If the correlating clonotypes are derived from a
populations study, there is no need for the calibration test and a
blood test at the time at which the objective disease activity is
to be assessed is sufficient to measure AutoImm Load in order to
inform the treatment decision.
Example 11
Measuring Response to Drug Therapy of an MS Patient
As stated above, one of the principle challenges in MS therapy is
measuring how well and whether a patient is responding to a drug
therapy. During progressive and late stage disease there are
clinical assessments such as the Expanded Disability Status Score
(EDSS) which measure the degree of physical impairment that has
resulted from the disease. However, these assessments are not
useful in early stage or relapsing/remitting disease. Clinical
parameters around relapses can be used to assess disease
progression, but these are coarse and lagging indicators, as
patients can go several years between relapses, during which little
evidence can be gleaned from clinical assessments. Lastly, brain
imaging such as gadolinium enhanced MRI can be used to examine
brain lesions. MS patients are typically given such an MRI on a
yearly basis. However, such images lack specificity. Furthermore,
as a measure on integrated brain damage, they are not good measures
of current disease activity but rather reflect the history of the
disease and its impact on the brain.
While it is true that the current clinical treatment paradigm for
MS is that patients diagnosed with relapsing remitting disease
should be under continuous therapy in order to delay the onset of
progressive disease, the increasing repertoire of approved drugs to
treat MS makes the lack of biological feedback increasingly
problematic. The list shown above of approved drugs to treat MS
continues to get longer as the substantial investment in MS
therapies begins to bear fruit. Each of these drugs has serious
side effects and is very expensive to administer, with costs from
$30,000-$100,000 per year of treatment. Patients that are not well
managed will sooner transition to progressive disease which is
debilitating and causes expensive health care interventions
including hospitalizations and long term care. Hence, the patient
can be allowed to receive optimal therapy early in treatment.
Clinical Utility Example
Patient profile: A 30 year old female comes to the hospital with
monocular visual impairment with pain. She is given a neurological
assessment and a lumbar puncture to obtain cerebral spinal fluid
which is used to assess whether clonal T cells are present. She
also is referred for a brain MRI. Based on these tests, a diagnosis
of MS is made. She is prescribed Betaseron 250 mcg per injection to
be self administered subcutaneously every other day. At a follow-up
visit six months later, the patient is complaining of depression
and weight gain. No further neurological events have been reported
to the physician. The doctor is now faced with a clinical dilemma.
Should the doctor maintain the therapy as it is been administered?
Should a new therapy be used? Should the doctor order an MRI
incurring cost and subjecting the patient to additional contrast
exposure? Should the doctor wait until the next scheduled MRI shows
new lesions? Should the doctor wait to see if flares recur? All of
these decisions would benefit from an unambiguous measure of
whether the disease is active or not.
AutoImm Load would be very helpful in this situation to assess the
response to therapy by measuring disease activity either alone or
in combination with other markers of disease activity. An algorithm
for AutoImm Load will be developed using the studies described
herein. The correlating clonotypes that will be used to calculate
AutoImm Load will be measured using a calibration test. This
calibration test will be done using blood from a patient at a time
of peak disease activity, for example at the start of therapy. The
calibration test could be performed using blood or alternatively
using the tissue that is affected (e.g. CSF). At a later time at
which the response to therapy is to be assessed, a blood sample can
be taken and used along with the calibration test to measure
AutoImm Load. This can be used to make a treatment decision. If the
correlating clonotypes are derived from a population study, there
is no need for the calibration test and a blood test at the time at
which the response to therapy is to be assessed is sufficient to
measure AutoImm Load in order to inform the treatment decision.
Example 12
Prediction of MS Flares
As in all autoimmune diseases, the amelioration of flares is a
principle goal of therapy. Not only are flares debilitating for the
patient and expensive to treat, but it is increasingly believed
that each flare contributes to longer term non reversible disease
progression. Several therapies can be used to control incipient
flares such as IV methylprednisolone or oral prednisone. Such
medications have significant side effects and as such are not
prescribed without evidence of an active flare. A measure of
increasing subclinical activity that was correlated with subsequent
clinical flares could be used to inform this sort of proactive
flare treatment which could result in shorter and less damaging
flares. In addition there are therapies that demonstrate high
clinical efficacy for reduction of flares that carry risks of very
significant and lethal of side effects. One such drug is Tysabri, a
drug that has been shown to result both in improved clinical
outcomes and to increase the risk of deadly brain infections such
as PML. These risks have reduced the value of such drugs to last
line therapy when other drugs are proving to no longer control
progression and limited the value of these drugs as chronic
treatments. A test that could predict when the flare state is
incipient could increase the utility of such drugs as they could be
used in a manner similar to steroids to control acute flare periods
while minimizing the risks of lethal side effects.
Clinical Utility Example
The patient from Example 11 is on Betaseron for 3 years and reports
a clinical flare that lasts a week. The patient's MRI at the end of
the year shows significant new lesions (multiple discrete variable
sized ovoid perpendicularly directed T2W and FLAIR hyperintense
lesions (plaques), appearing iso-hypointense on T1W images and
hyperintense on T2W images involving bilateral periventricular and
subcortical white matter regions, including the calloso-septal
interface). The doctor is concerned that the patient is at high
risk of flares over the course of the next 12 months. A clinical
dilemma presents itself. Does the doctor wait for further clinical
symptoms to intervene with additional therapy? Should the doctor
switch therapies? If so, should another class of injectable be used
such as copaxone or should a new class of therapy be used such as
Tysabri? Should steroids be prescribed? A test that could monitor
sub clinical disease activity and show when the disease is
increasing and when a flare is likely to result could be used to
help make these clinical decisions.
AutoImm Load would be very helpful in this situation to assess the
risk of flare by measuring disease activity either alone or in
combination with other markers of disease activity. An algorithm
for AutoImm Load could be developed using the studies described in
this invention. The correlating clonotypes that will be used to
calculate AutoImm Load could be measured using a calibration test.
This calibration test could be done using blood from a patient at a
time of peak disease activity, for example at the start of therapy.
The calibration test could be performed using blood or
alternatively using the tissue that is affected (e.g. CSF). At a
later time at which the risk of flare is to be assessed, a blood
sample can be taken and used along with the calibration test to
measure AutoImm Load. This can be used to make a treatment
decision. If the correlating clonotypes are derived from a
population study, there is no need for the calibration test and a
blood test at the time at which the flare risk is to be assessed is
sufficient to measure AutoImm Load in order to inform the treatment
decision.
Example 13
Monitoring Therapy Compliance for MS
Because of the relative infrequency of clinical symptoms in the
early stages of the disease, the interactions between a patient and
his or her physician are not very frequent. At the same time, the
therapies that are being prescribed are both expensive and
inconvenient for the patient, involving self injections that can
cause painful reaction and side effects. There is as a result a
significant degree of non compliance with therapeutic regimes which
are hard for a physician to monitor as the interactions between the
patient and doctor is not routine. A test that could measure the
state of the sub clinical disease would allow both doctor and
patient to see on a routine basis how well controlled the
underlying disease is. Such methods have proved very effective in
HIV patients in motivating them to pursue therapy effectively. A
test blood test that was performed quarterly would allow the
physician to see the patient and measure the state of the
disease.
AutoImm Load would be very helpful in this situation to assess the
compliance with therapy by measuring disease activity either alone
or in combination with other markers of disease activity. An
algorithm for AutoImm Load will be developed using the studies
described herein. The correlating clonotypes that will be used to
calculate AutoImm Load will be measured using a calibration test.
This calibration test will be done using blood from a patient at a
time of peak disease activity, for example at the start of therapy.
The calibration test could be performed using blood or
alternatively using the tissue that is affected (e.g. CSF). At a
later time at which the compliance with therapy is to be assessed,
a blood sample will be taken and used along with the calibration
test to measure AutoImm Load. This will be used to make a treatment
decision and to better guide the patient toward better compliance.
If the correlating clonotypes are derived from a population study,
there is no need for the calibration test and a blood test at the
time at which the compliance with therapy is to be assessed is
sufficient to measure AutoImm Load in order to inform the treatment
decision.
Example 14
Amplification of Mouse TCR.beta. and IgH Sequences
An amplification and sequencing scheme for mouse TCR.beta. and IgH
will be developed that is similar to that developed for humans.
Similar methods to minimize the differences in amplification
efficiency of different sequences and similar validation techniques
using spikes and the 5' RACE technique described above will be
applied. The minimum input amount of cDNA will be determined in a
similar methodology as described for human samples. One difference
in the amplification scheme between mouse and humans is that the
two C segments for TCR.beta. in mouse do not have any polymorphisms
in the 50 bp closest to the J/C junction. Therefore, in the scheme
the primer for the first stage amplification will be placed at
positions 25-50 and for the second stage amplification the primer
will be placed at positions 1-25, and the primer will have a 5'
tail for the latter primer containing the P5 sequence. The
different sequences will improve specificity and is similar to the
strategy used in humans except there is no need to "loop out" any
bases for polymorphisms.
Example 15
Primary Analysis of Mouse Sequence Data
The analysis framework that will be used for analysis of mouse data
is similar to that described above for the human data. One
difference is that the mouse samples will be sequenced to less
depth than the human samples. It is anticipated that the blood
samples from the mouse will be 100 .mu.l. In 100 .mu.l of blood
there are .about.100K lymphocytes and hence sequencing to a depth
much higher than 100K does not significantly improve the precision.
Therefore, only 100K reads for each mouse sample will be obtained.
Even though the number of reads will be smaller for mouse than
humans, a larger fraction of mouse total and blood lymphocytes will
be sampled. The number of total mouse lymphocytes is expected to be
more than 3 orders of magnitude smaller than that of humans.
Similarly 100 .mu.l of blood will provide a better sampling
(.about.10%) of the lymphocytes in the mouse blood at the time when
compared to sampling obtained using 10 ml of human blood
(0.2%).
Example 16
IgH and TCR Repertoire Analysis in Mouse SLE Model
A mouse model of SLE will be used to study the relationship between
TCR/BCR repertoire and disease activity. The mouse model will be
the B6 with the sle1 and sle3 loci from NZM2410. These B6.sle1.sle3
(BSS) mice develop SLE-like nephritis in a spontaneous fashion.
Three types of cohorts will be studied. For all study points, blood
BUN, creatinine, and anti-nuclear autoantibodies, urine protein,
and creatinine level will be obtained. It will be determined
whether a score generated from blood TCR/BCR repertoire correlates
well with these measured indices of kidney disease. The first
cohort will be similar to the human cohort described where
longitudinal blood samples will be collected along with kidney
function assessment. Specifically, 7 BSS mice will be followed on a
monthly basis till month 8. At the end, these mice will be
sacrificed and in addition to blood, spleen and kidney tissue are
analyzed. As a control, 5 B6 mice will be assessed in a similar
manner. The second cohorts will be cross sectional where different
cohorts of animals will be sacrificed at specific times and spleen,
kidney, and blood samples will be analyzed at that time.
Specifically, 5 BSS mice will be sacrificed each month and blood,
spleen, and kidney will be analyzed. As a control, two B6 control
mice will be assessed in the same fashion. Finally a third cohort
will be treated with steroids after disease onset and nephritis
assessment and blood samples obtained on a regular basis after
that. Specifically at 4 months of age, 20 mice that have the
disease will be treated with steroids and then on a biweekly basis
for the next 4 months blood is taken for TCR/BCR repertoire
analysis and kidney function assessment. As a control 5 BSS mice
will be treated with placebo and followed in a similar fashion. TCR
and BCR repertoire analysis will be performed from all the study
points (i.e. different time points and different tissues for the
same time point). The analysis will involve 2 stage PCR, sequencing
processing, and primary data analysis as described above.
Example 17
Identification and Dynamics of Clonotypes that Correlate with Mouse
SLE
First, a set of clonotypes that correlate with renal function will
be identified. As a measure of renal function, urine
protein/creatinine ratio, serum creatinine, or BUN levels can be
used. In the first and third cohorts, the correlation of the blood
level of each HPC clonotype with each of the three measures can be
assessed. In a similar manner to what is described in humans, it
can be assessed whether there is a great increase in the number of
clonotypes with high correlation to 1, 2, or all 3 of the renal
function measures over random expectation (or permutation testing).
Given that random expectation, the correlation threshold will be
picked where only 10% of the clonotypes with a correlation level
above that threshold are expected to have the observed correlation
level by chance (10% false discovery). These clonotypes will be
focused on, and this set will be defined as "correlating
clonotypes".
In addition to this statistical method to identify correlating
clonotypes, clonotypes might be identified relevant to disease by a
"functional" method of enrichment of specific clonotypes in kidney
tissue. By the functional method a set of clonotypes may be
identified in cohort 2 that may be relevant to disease, and these
will be called functionally-identified correlating clonotypes. The
extent of overlap between the "statistical" definition and the
"functional" definition of correlating clonotypes can be assessed.
Cohorts 1 and 3 have kidney samples collected at the last time
point. It can be assessed whether clonotypes enriched in these
kidney samples are present in the blood and are among the
clonotypes with higher correlation with renal function.
The dynamics of correlating clonotypes (statistically and
functionally identified) can then be evaluated. For example, using
data from cohort 2, the time course of the rise and fall (if any)
of their levels will be evaluated in the three compartments:
kidney, blood, and spleen.
In the statistically identified correlating clonotypes, a subset of
the correlating clonotypes would be identified by virtue of their
correlation with renal function. The correlating clonotypes can be
identified without knowing the renal function data. In other words,
the characteristics that distinguish the correlating clonotypes
from those that are irrelevant to disease can be understood. In
order to do that a set of clonotypes with low correlation to renal
function will be identified as control non correlating
clonotypes.
Characteristics of Clonotypes that Correlate with Disease
After identification of the two sets of clonotypes, correlating and
not correlating, characteristics that distinguish these two sets
will be searched for. Separate and combined analysis using the
correlating clonotypes identified statistically and functionally
will be performed. The same type of characteristics studied in
humans will be assessed, for example the level of the clonotype,
the presence of particular sequence motifs, and the sequence of
other related clonotypes. As described for the human study, there
is a significant risk of overfitting and hence cross validation
technique or separate training and testing sets need to be
employed.
One utility for the mouse experiment is the availability of cells
allowing for assessment of whether correlating clonotypes are
enriched in a specific subtype of cells. It will be studied whether
correlating clonotypes are enriched in some cell subtypes;
sequencing from the full set of lymphocytes and from the specific
subtype where correlating clonotypes are enriched can be done, and
this criteria of enrichment can be used as an extra characteristic
to distinguish correlating clonotypes from other disease-irrelevant
clonotypes. In order to know what cell subtypes clonotypes are
enriched a couple approaches will be taken: hypothesis driven and
hypothesis free. The first is to try a dozen candidate surface
markers on T or B cells in a set of samples. For example, one
candidate is CD69 on T cells to select activated T cells. For B
cells studies have shown the increase of CD27.sup.high cells in
active SLE, and therefore that is a good candidate for a marker of
cells that may have enrichment of the correlating clonotypes. In
each of these experiments, the specific cell subtypes is purified
through FACS. Then a sequencing reaction is done for cDNA from the
full complement of the lymphocytes as well as for cDNA from the
lymphocytes that were purified by FACS from a collection of
different samples. It will be assessed whether the two sets of
correlating and non correlating clonotypes are present in different
proportions in the full complement of lymphocyte compared to the
FACS purified subset. Markers that have a large difference can be
useful in identifying correlating clonotypes. Enrichment of
clonotypes in subtypes of cells with these markers will be used in
addition to the sequence parameters to detect correlating
clonotypes.
In the hypothesis free approach, markers will be searched for which
are differentially expressed in cells with a correlating clonotype
from other cells. A few cases will be chosen where a specific TCR
clonotype is clearly correlating with disease, and cases will be
picked where that clonotype is highly enriched that it represents
the majority of the clonotypes with the same V segment. FACS will
be done using antibody to the specific V segment (antibodies
against all V segments are commercially available) to select a
population that is highly enriched for cells carrying the
correlating clonotype. The RNA can be prepared from these cells and
the expression of all the genes can be studied by performing an
array experiment. As a control, total RNA from lymphocytes can be
used and/or RNA from FACS purified cells carrying another
irrelevant V segment. Markers that maximally distinguish the sample
obtained from the FACS purified V segment with the correlating
clonotype from the controls can be searched for. Markers, including
surface markers (since it is much easier to do FACS with surface
proteins) that distinguish the two populations can be found. If a
consistent RNA marker from samples of several mice is observed it
will be validated at the protein level. Using the same samples,
antibodies against the marker protein will be used in a FACS assay
to purify cells carrying the marker protein. More than one marker
may be tested to increase the chance of validating one of them. The
TCR and/or BCR from the purified cells will be sequenced. If the
RNA results hold at the protein level then the correlating
clonotypes should be enriched in the purified subset of cells.
After validating that RNA results still hold at the protein level,
the results will be validated in other samples. Samples that were
not subject to the array analysis will be subjected to FACS
analysis using the antibody to the marker protein(s). The TCR
and/or BCR of the purified cells will be sequenced. It will be
evaluated whether the correlating clonotypes are enriched in the
cells purified using antibody to the specific marker(s). This will
validate the utility of the marker(s) in the identification of
correlating clonotypes.
Example 18
Use of IgH and TCR.beta. Repertoire to Measure Disease Activity
The algorithm for correlating clonotypes from above can be applied
to identify in all samples of cohorts 1 and 3 correlating
clonotypes by virtue of their sequence and/or markers. Using the
level of the correlating clonotypes in each patient, an AI score
can be generated that correlates with a measure of renal function.
As described above, there is an overfitting risk and the cross
validation technique and/or separate training and testing set need
to be employed. The correlation of AI and renal function measures
can be evaluated in a cross sectional manner (all study points of
all mice). The question of whether the AI score changes in an
individual mouse can also be evaluated when renal function changes.
This can be evaluated by comparing the AI from high and low renal
function in the same animal in a similar manner to what is
described in humans.
Example 19
Linking of Sequences from the Same Cell
Two sequences can be amplified from the same cell, and during
amplification they can be linked to form one amplicon. Information
on the presence of these two sequences in the same cell can then be
preserved even if the linked sequences are mixed with a pool of
sequences from other samples.
An example of the utility of this linking scheme is for assessment
of the diversity of TCRs. The diversity of TCR is generated from
the diversity of each of TCR.alpha. and TCR.beta.. In addition, the
combination of a TCR.alpha. and TCR.beta. in a cell adds
significantly to the diversity. However, when nucleic acids are
extracted from a sample with a plurality of T-cells, the
information of which TCR.alpha. is present in the same cell as
TCR.beta. is lost. A method that allows the preservation of this
information is presented here. This method comprises separating the
cells in distinct compartments, amplifying the desired sequence in
a way that covalently links initially separate amplicons, and
optionally mixing all the amplified sequences for later analysis.
Several methods can be conceived to place each cell in a
compartment. For example, one method is to put cells in a
microdroplet or a micelle emulsion that can be used in PCR. These
droplets can be filled in a directed manner or randomly filled in
such a way that most droplets contain at most a single cell. Also,
cell sorting can be used to place a single cell in a PCR container.
Amplification of nucleic acid can then be performed in each
droplet.
Scheme 1
As illustrated in FIG. 9, sequence 1 can be amplified using primer
1 and primer 2. Primer 2 carries a 5' overhang sequence that is not
complementary to the genomic sequence (FIG. 9A, thin line).
Similarly sequence 2 can be amplified using primer 3 and primer 4
(FIG. 9A). Primer 3 carries a 5' overhang sequence that is
complementary to the overhang sequence of primer 2 (FIG. 9A, line
dashed line). In this figure the two overhangs (or the two linking
sequences) representing two complementary sequences are drawn in
thin lines; one sequence is shown as a solid line and its
complement is shown as a dashed line. Other complementary sequences
are drawn to have the same solid colors: black, and grey for
sequence 1 and 2, respectively.
After amplification with primers 1-4, each of the two amplification
products has a linking sequences on one end and the two products
can anneal to each other and strands can be extended to form a full
double stranded molecule (FIG. 9B). This molecule now has sequence
1 and 2 linked to each other and can then be amplified with primers
1 and 4 (FIG. 9C).
All 4 primers can be put in the reaction at the same time to
achieve sequence linking and amplification. It may be beneficial to
add low concentration of primers 2 and 3. The low concentration of
primer 2 and 3 will ensure that the two individual sequence
amplicons will reach saturation early in the reaction allowing the
linked amplicon to dominate the PCR reaction in the latter stages
of the reaction. This will lead to the final reaction having a high
concentration of the linked amplicon relative to the individual
sequence amplicons.
Scheme 1(a)
Scheme 1(a) is a variant of Scheme 1 in which the linking sequence
is identical to the primer 2 sequence (FIG. 10). Sequence 1 can be
amplified using primer 1 and primer 2 with no overhanging sequences
on the primers (FIG. 10A). Primer 3 carries a 5' overhang sequence
that is complementary to primer 2 (FIG. 10A). Sequence 2 can be
amplified using primer 3 and primer 4 creating a linking sequence
that is complementary to Sequence 1 (FIG. 10A). Other complementary
sequences are drawn to have the same colors: black, and grey for
sequence 1 and 2, respectively.
After amplification with primers 1-4, the two products can anneal
to each other via the Primer 2 sequence and strands can be extended
to form a full double stranded molecule (FIG. 10B). This molecule
now has sequence 1 and 2 linked to each other and can then be
amplified with primer 1 and 4 (FIG. 10C).
Scheme 2
Scheme 2, shown in FIG. 11 is a similar scheme to scheme 1 except
that the ultimate amplification is achieved with sequences that are
not complementary to the genome. One advantage of this approach is
that the priming sequences can be chosen to be ideal for
amplification with no off target amplification. This can be helpful
in cases where primers complementary to the genomic sequence to be
amplified are not ideal. By using primers not complementary to the
genome for amplification, low concentration of primers 1-4 can be
used, minimizing off target amplification. Also, scheme 2 can be
adapted to a multiplexing scheme in which more than a pair of
primers is used without causing as many primer interactions. Each
pair of sequences to be linked will have its own unique 4 primers
that need not be at high concentration. One pair of amplification
primers can amplify all the pairs of linked sequences (FIG.
11C).
Sequence 1 can be amplified using primer 1 and primer 2 (FIG. 11A).
Primer 1 and 2 carry on their 5' ends distinct overhang sequences
that are not complementary to the genomic sequence (FIG. 11A,
dotted and thin lines, respectively). Similarly, sequence 2 can be
amplified using primer 3 and primer 4 (FIG. 11A). Primer 3 and 4
carry on their 5' ends distinct overhang sequences that are not
complementary to the genomic sequence (FIG. 11A). The overhang on
primers 1 and 4 are labeled as "Amp 1" (dotted) and "Amp 2" (wavy)
and are sequences not complementary to the genome ultimately used
for amplification (FIG. 11A). Analogously to scheme 1, the
overhangs of primer 2 (thin) and 3 (thin/dashed) are the linking
sequences that are complementary to each other. Other complementary
sequences are drawn to have the same colors: black and gray for
sequence 1 and sequence 2, respectively.
After amplification with primers 1-4, each of the two amplification
products has a linking sequences on one end and the two products
can anneal to each other and strands can be extended to form a full
double stranded molecule (FIG. 11B). This molecule now has sequence
1 and 2 linked to each other and can then be amplified with primer
5 and 6 (FIG. 11C).
Optionally, primers 1-4 can initially be used, and after the
linking of the two sequences, primer 5 and 6 can be added. A more
preferred embodiment wilt have all the primers added in the first
step. Yet a more preferred embodiment will have all the primers
present initially with the concentration of primers 1-4 lower than
that of 5 and 6. This allows the full linking and amplification to
occur in one step. The low concentration of primers 2 and 3 will
ensure that the two individual sequence amplicons will reach
saturation early in the reaction allowing the linked amplicon to
dominate the PCR in the latter stages of the reaction. This will
lead to the final reaction having a high concentration of the
linked amplicon relative to the individual sequence amplicons.
Furthermore, the low concentration of primers 1-4 minimizes any off
target amplification that can occur if these primers were lower
quality than primers 5 and 6.
The use of primers 5 and 6 for amplification enables more efficient
multiplexing (FIG. 12). One pair of primers (primers 5 and 6) can
be used to amplify all the linked sequences. The linking sequences
can be designed in different ways for different applications. The
example illustrated in FIG. 12 is for two pairs of sequences to be
linked, but this scheme can be extended further to 10's, 100's, or
1000's of sequences. If there is a set of gene pairs to be linked
(e.g., TCR.alpha. with TCR.beta. and IgH with IgK) then the linking
sequences for each pair can be different. In this example linking
sequencing for TCR.alpha. and .beta. will be different from those
of IgH and IgK as depicted by thick dashed lines (TCR.alpha. and
TCR.beta.) or thin dashed lines (IgH with IgK) (FIG. 12A). All the
amplified sequences in this example are shown in the same color.
The amplification primers for the all the linked sequences will be
the same primers: 5 and 6 as depicted in FIG. 11. In other
applications the same linking sequences can be used if there is no
specific pairing.
It is also conceived that more than 2 sequences can be linked. For
example 3 or more sequences can be linked together (FIGS. 13A-13D).
To create a molecule that links 3 sequences, one of the products
can have two different linking sequences on its ends, each linking
with one product (FIG. 13A). In the depicted example, sequence 2
has two linking sequences. The linking sequence of primer 3 allows
the linking to sequence 1 through the linking sequence of primer 2
(linking sequence complementary pair LS1). Similarly, the linking
sequence of primer 4 allows the linking to sequence 3 through the
linking sequence of primer 5 (linking sequence complementary pair
2, LS2) (FIG. 13A). In another cycle the whole of sequence 2
becomes a linking sequence to link sequence 1 and sequence 3. The
Amp 1 and Amp 2 sequences complementary to primers 1 and 6 enable
amplification after formation of a molecule with linked sequences
1-3.
Example 20
Monitoring for Metastatic Recurrence in Colon Cancer Patients
Many cancers that are detected at a treatable stage still carry an
ongoing risk to the patient of metastatic tumor recurrence. Such
recurrences are often detected late and at untreatable stages an
can be fatal to the patients. One example of such a situation is
that of recurrent colon cancer. Despite increasingly aggressive
colon cancer screening programs, colon cancer represents one of the
most common malignancies in the US. Approximately 150,000 patients
per year are diagnosed with colon cancer at serious but treatable
stages (Stage II and Stage III). These patients are treated by
tumor resection followed by a course of chemotherapy. While these
treatments are generally effective, there is nonetheless a
significant chance that these patients will have metastatic
recurrences of the primary tumor in the years following treatment.
50% of Stage III patients for instance will have a recurrence
within 5 years of surgery. These recurrences can be either isolated
(e.g. in the colon or liver) or multifocal. In either case but
particularly if they are isolated, detecting them at an early stage
can play a role in maximizing the chances of successful therapy
(surgery and/or chemotherapy).
There are currently two tests used in post treatment surveillance.
CT scan of the abdomen and chest is used to identify tumors visible
on these images. Typically these scans are done at intervals of
6-12 months for the first 5 years post therapy. While these scans
can reveal early stage malignancies, there clinical effectiveness
is in debate. Drawbacks of these scans include the fact that they
subject the patients to significant amounts of radiation which can
itself cause further tumors and the significant expense. Another
blood based test has been shown to have some value: CEA testing.
This antibody test measures the level of a protein in scrum that is
specific to some colon tumors. The drawback to CEA testing is its
lack of sensitivity (<60% of patients with positive CT scans
have a positive CEA test).
In this embodiment of the invention, lymphocytes obtained from the
resected primary tumor are used to develop an immune profile that
can be used to add sensitivity to a blood based test for early
cancer recurrence TCRs (and/or BCRs) of the lymphocytes found in
the resected tumor can be amplified and sequenced. Clonotypes that
are enriched in the tumor sample are likely relevant to the immune
response to the tumor. Subsequent blood draws from the patient can
be used to assess the level of these clonotypes. A rise in the
level of these clonotypes can signal an immune response to a tumor
recurrence. In this case the detection of the immune response may
be more sensitive than the detection of the tumor marker
itself.
Discovery Study for the Detection of Cancer Recurrence Using a
Calibration Test
It is conceived that a discovery study can be performed to
determine the likelihood of detection of recurrence given the
profile of blood TCR (and/or BCR). Samples of resected tumor
samples as well as follow up blood samples of patients with known
outcome can be used for this study. TCR (and/or BCR) from all these
samples can be sequenced. Candidates for the correlating clonotypes
are those that are present in the TCR (and/or BCR) data from the
tumor samples Given the known outcomes in this training study one
can devise using the standard cross validation techniques, a model
that generates a score (Recurrence Risk) given the level of the
different clonotypes. This Recurrence score can thus be calculated
in a new patient by measuring the clonotypes in the resected tumor
(calibration point) and the data from the clonotypes found in the
same patient's blood at a later time during the surveillance for
recurrence. The use of the tumor data allows great reduction in the
number of clonotypes present in blood that are considered in this
analysis.
Discovery Study for the Detection of Cancer Recurrence Using a
Calibration Test and a Population Study
It is likely that not all clonotypes that are enriched in the tumor
specimen are relevant to the immune response to the tumor. There
might be some lymphocyte that expanded locally due to a favorable
inflammatory condition. In another embodiment of this invention the
discovery study can be done using the same samples but the study is
used to identify parameters that distinguish "correlating" from
"non correlating" clonotypes. These parameters can include 1)
Sequence motif: The motif can be a specific V or J region, a
combination VJ, or short sequences in DJ region that is associated
with a clonotype being correlating; 2) Size of the clonotype; 3)
Level: Absolute level (number of reads per million) or rank level;
4) Similarity to other clonotypes: the presence of other highly
related clonotypes, like those with silent changes (nucleotide
differences that code for same amino acids) or those with
conservative amino acid changes; 5) For the BCRs the level of
somatic mutations in the clonotype and/or the number of distinct
clonotypes that differ by somatic mutations from some germline
clonotype. 6) Presence in a cell carrying a specific marker. This
study will then result in an algorithm that can predict which
clonotypes are likely to be correlating with cancer recurrence in
blood given a specific set of clonotypes present in a given tumor
sample. These clonotypes can then be used to develop a score of
Recurrence Risk in the same manner as described above.
Discovery Study for the Detection of Cancer Recurrence Using a
Population Study
In another embodiment of this invention, the clonotypes measured in
the resected tumor are used to generate a model that predicts
correlating clonotypes in as yet unseen samples. This model can
also be used to generate a Recurrence Risk score in a manner
analogous to that described above. In this model there would be no
need to measure the clonotypes in the resected cancer tissue in a
new patient undergoing recurrence surveillance but rather the
Recurrence Risk could be assessed by simply measuring the
clonotypes in a given blood sample.
Discovery Study for the Detection of Primary Colon Cancer Using a
Population Study
As an extension it is conceived that detection of primary cancers
can be achieved using the same methodology. With the primary
cancers there is no tumor resected that can be used to enrich for
relevant clonotypes. However, even in the presence of tumor
resection data it is conceived that additional sequence and other
parameters need to be used to identify relevant clonotypes and
ultimately generate a score for likelihood of cancer detection.
Therefore by extension if the algorithm is predictive enough one is
able to detect the cancer from blood (or other bodily fluid)
without the data from the resected tumor. In this embodiment of the
invention, a discovery study with blood samples from patients
preceding their diagnosis of primary cancer need to be available.
In an analogous fashion to the one described above, parameters
(sequence and other) can be identified to predict the clonotypes
that are correlated to the immune system response to the tumor. A
model can then be used to generate a Cancer Risk score that
predicts the progression risk to colon cancer. This algorithm can
then be applied to new patient's blood sample to measure the risk
of primary colon cancer.
Example 21
Monitoring for Rejection in Heart Transplant Patients
Heart transplants are a relatively uncommon procedure as the supply
of organs is very limited. 3,500 heart transplants performed every
year worldwide. Each procedure is very expensive and the organs
that are used are priceless. As a result the patients that receive
these organs are treated extremely proactively. In order to measure
the state of the immune reaction to the donated organ at a time at
which interventions with immunosuppressants can be effective,
patients are given periodic heart biopsies to measure inflammation
of the organ. Based on these tests, aggressive courses of
immunosuppressants may be given. These procedures have several
limitations. As invasive surgical procedures they have risks to the
patient. Furthermore they are expensive and can only be done at
infrequent intervals. A blood based tests based on profiling the
expression of a panel of 11 test genes (Allomap) have been shown to
be quite sensitive in detecting organ rejection but lacks
sufficient sensitivity to be used as a replacement for biopsy and
is instead used to decide when to do a biopsy. In one embodiment of
this invention TCR (and/or BCR) profiles are used to assess the
state of "rejection" and generate a Rejection Risk score that
predicts the likelihood of rejection in a specific time frame. It
is conceived that a discovery study can be performed to determine
the likelihood of rejection given the profile of blood TCR (and/or
BCR). This can be used in the clinic to inform the
immunosuppressive therapies that are being used.
Discovery of Correlating Clonotypes Using a Population Study
In this embodiment of the invention a population of post transplant
patients with blood samples with known clinical outcome can be
used. TCR (and/or BCR) from all these samples can be sequenced and
correlation of individual clonotypes with rejection outcome can be
used to distinguish correlating from non-correlating clonotypes.
Subsequently, parameters can be derived that distinguish those two
classes of clonotypes. These parameters can include 1) Sequence
motif: The motif can be a specific V or J region, a combination VJ,
or short sequences in DJ region that is associated with a clonotype
being correlating; 2) Size of the clonotype; 3) Level: Absolute
level (number of reads per million) or rank level; 4) Similarity to
other clonotypes: the presence of other highly related clonotypes,
like those with silent changes (nucleotide differences that code
for same amino acids) or those with conservative amino acid
changes; 5) For the BCRs the level of somatic mutations in the
clonotype and/or the number of distinct clonotypes that differ by
somatic mutations from some germline clonotype. 6) Presence in a
cell carrying a specific marker. An alternative or supplemental
method to define the correlating and non-correlating clonotype
would come if the study samples have biopsy samples of the graft,
particularly if it was in active rejection. It is expected that at
that time there will be great enrichment of the correlating
clonotypes. Parameters to distinguish these from the other
clonotypes can be identified as discussed above.
The profile data from the blood samples is then used to predict the
likelihood of rejection. Given the known outcomes in this training
study one can devise, a model using the standard cross validation
techniques that generates a Rejection Risk score given the level of
the different clonotypes. Given the profile in a new blood sample
of TCR (and/or BCR) at a specific point a Rejection Risk score
relating to the likelihood of rejection can be generated
Discovery of Correlating Clonotypes Using a Calibration Test
In another embodiment a method of identifying correlating
clonotypes can be implemented using a calibration test for each
patient. This method involves a first biopsy sample be taken post
transplant. The presence of biopsy material of the graft post
transplant offers the possibility of analyzing TCRs from the biopsy
sample to identify the correlating clonotypes as defined by those
that are prevalent in this sample. This set of clonotypes can then
be followed in blood and a score is generated for the likelihood of
rejection. The algorithm to generate the Rejection Risk score is
derived through a discovery study that is similar to the one
described above that utilizes the available clinical data and the
levels of the correlating clonotypes to generate a Rejection Risk
score that approximates the likelihood of rejection.
In this embodiment a specific calibration test will be done using
material from a first biopsy post transplant but further biopsies
could be replaced by the use of blood samples whose clonotypes
could be used along with this calibration test to measure a
Rejection Risk score.
In addition to the graft biopsy, one can use the blood samples
before transplant as another calibration point. Clonotypes that are
prevalent in this sample are unlikely to be related to the
rejection representing rather the history of prior antigens the
patient has seen. Therefore when considering the blood samples
after transplant one can subtract the clonotypes that were present
before the transplant in determining the correlating clonotypes.
These clonotypes can then be used to generate a model of Rejection
Risk.
In this embodiment, two calibration tests would be can be used: one
prior to transplant and one from a biopsy after transplant. These
calibrations could then be used along with clonotypes derived from
a blood test to measure Rejection Risk.
Discovery of Correlating Clonotypes Using a Calibration Test and a
Population Study
In another embodiment, the identification of the correlating
clonotypes can be achieved through a combination of the above
approaches. Specifically this can be achieved by using the
population study to generate an algorithm to predict correlating
clonotypes. In addition it can be achieved through calibration data
from the same patient using graft biopsy and/or blood samples
pre-transplant. A more preferred embodiment will employ both
approaches: population-built algorithm and individual calibration
to most accurately identify the correlating clonotypes. A Rejection
Risk score is then generated using the level of these clonotypes to
predict the likelihood of rejection through the use of the
population study as a training set.
In this embodiment, two calibration tests can be used: one prior to
transplant and one from a biopsy after transplant. These
calibrations could then be used along with clonotypes derived from
a blood test to measure Rejection Risk.
The prediction of GVHD can be done in a very similar manner with
the same concept of the population study to generate an algorithm
to predict correlating clonotypes. Also the "negative" calibration
can be generated from the donor sample pre-transplantation. An
approach using both the algorithm and calibration is likely to be
more predictive of the correlating clonotypes. An algorithm to
compute a score of the likelihood of GVHD given the level of the
correlating clonotypes can be generated using a population study in
a manner as described above. This algorithm can then be used for
the prediction of the likelihood of GVHD in the next set of
patients.
Example 22
Monitoring for PML Infection in Ms Patients Treated with
Natalizumab
One embodiment of the invention uses TCR and/or BCR profile to
detect subclinical Progressive Multifocal Leukoencephalopathy (PML)
in MS patients. PML is a serious and often fatal disease that
causes often rapidly progressive demyelinating disease through
killing oligodendrocytes that synthesize myelin. It is caused by JC
virus that is present in a latent phase in the majority of the
population. In a fraction of the immunosuppressed population (e.g.,
AIDS) the virus is reactivated leading to the development of this
serious disease. In addition some patients who are being
immunosuppressed through the use of medication like post transplant
patients can also develop PML. Some specific medication has been
linked to the risk of PML in specific patient populations. For
example natalizumab (Tysabri) was associated with the development
of more than 10 cases of PML among patients with multiple sclerosis
(MS) leading to its withdrawal of the market for a period of time.
Natalizumab is well accepted to be more effective than the other
FDA approved medications for multiple sclerosis, but its use has
been limited by the fear of PML development. Once PML is suspected,
plasmapheresis can be performed to reduce the concentration of the
drug in the patient. The overlap between symptoms of MS and PML can
sometimes delay the detection of PML. Early detection of
subclinical PML is urgently needed.
These clonotypes may be discerned from blood samples from a
population where some patients developed PML. This population can
be used to identify clonotypes that correlate with the later
development of PML. With the availability of these clonotypes an
algorithm to identify parameters that distinguish these from other
clonotypes can be generated.
Discovery of Correlating Clonotypes Using a Population Study
In this case an algorithm is generated to predict the clonotypes
that are relevant to the emergence of PML. The algorithm can be
trained on a set of clonotypes deemed to be correlating with the
disease. In this embodiment of the invention blood (or other body
fluid) samples in a discovery study from a population of patients
with a latent infection with JC virus some of whom go on to develop
PML can be used. TCR (and/or BCR) from all these samples can be
sequenced and correlation of individual clonotypes with infectious
agent reactivation outcome can be used to distinguish correlating
from non-correlating clonotypes. Parameters that distinguish those
two classes of clonotypes can be identified. These parameters can
include 1) Sequence motif: The motif can be a specific V or J
region, a combination VJ, or short sequences in DJ region that is
associated with a clonotype being correlating; 2) Size of the
clonotype; 3) Level: Absolute level (number of reads per million)
or rank level; 4) Similarity to other clonotypes: the presence of
other highly related clonotypes, like those with silent changes
(nucleotide differences that code for same amino acids) or those
with conservative amino acid changes; 5) For the BCRs the level of
somatic mutations in the clonotype and/or the number of distinct
clonotypes that differ by somatic mutations from some germline
clonotype. 6) Presence in a cell carrying a specific marker. An
alternative or supplemental method to define the correlating and
non-correlating clonotype would come from a set of patients who are
mounting an immune response to the same infectious agent. Enriched
clonotypes (particularly those that are at a significantly higher
level than before the immune response) in these patients can be
considered correlating and parameters that distinguish them from
other clonotypes can be identified.
Similarly the correlating clonotypes can be identified from samples
of patients with active PML or from in vitro studies to identify
clonotypes that respond to JC virus antigen. The responding
clonotypes may originate from one or a plurality of subjects that
may be healthy or infected with the infectious agent. These
clonotypes can be considered correlating and parameters that
distinguish them from other clonotypes can be identified.
The profile data from the samples in the discovery study is then
used to predict the likelihood of reactivation. Given the known
outcomes in this training study one can devise using the standard
cross validation techniques, a model that generates a PML Risk
score given the level of the different clonotypes. So given the
profile in a blood sample of TCR (and/or BCR) at a specific point a
score relating to the likelihood of reactivation can be generated.
This algorithm can now be used with data from a novel patient to
predict the patient's correlating clonotypes as well as to generate
a PML Risk score for the likelihood of reactivation.
In a very similar manner other infection-related outcomes can be
studied. For example in addition to reactivation of latent
infection, one can assess clearance of infection. Furthermore given
the TCR and/or BCR repertoire one may be able to evaluate
likelihood of having immunity for a specific infectious agent.
Example 23
Monitoring for Reactivation of Latent Infections
In another embodiment TCR and BCR profiling can be used to monitor
infections that have periods of acute infection followed by latency
and reactivation. Examples of such diseases include Hepatitis B and
C as well as Herpes viruses. Predicting infections at early stage
would be desirable.
Discovery of Correlating Clonotypes Using a Calibration Test
In another embodiment a method of identifying correlating
clonotypes can be implemented using a calibration test for each
patient. The presence of a biological sample from the same patient
at a previous time point when the patient was mounting an immune
response to the infectious agent can serve to identify the
correlating clonotypes. This set of clonotypes can then be followed
in blood and a Reactivation Risk score is generated for the
likelihood of reactivation. The algorithm to generate the score is
derived through a discovery study that is similar to the one
described above that utilizes the available clinical data and the
counts of the correlating clonotypes to generate a Reactivation
Risk score that approximates the likelihood of reactivation. To use
this score a sample taken from a new patient in clinical practice
during a period of acute infection. This data would be used along
with a subsequent sample taken during the latent period to measure
the Reactivation Risk for clinical purposes.
Discovery of Correlating Clonotypes Using a Calibration Test and a
Population Study
In another embodiment, the identification of the correlating
clonotypes can be achieved through a combination of the above
approaches. Specifically this can be achieved by using the
population study to generate an algorithm to predict correlating
clonotypes. The correlating clonotypes can be obtained from a
population study of patients with known outcome of the infection
and/or a set of patients with active immune response to the
infectious agent, and/or from in vitro experiments to identify
clonotypes reactive with the infectious agent. In addition it can
be achieved through calibration data from the same patient using
older data points at the time of an active immune response against
the relevant infectious agent. A more preferred embodiment will
employ both approaches: population-built algorithm and individual
calibration to most accurately identify the correlating clonotypes.
A Reactivation Risk score is then generated using the level of
these clonotypes to predict the likelihood of reactivation through
the use of the population study as a training set. To use this
score a sample taken from a new patient in the clinic during a
period of acute infection is profiled. This data would be used
along with a subsequent sample taken during the latent period to
measure the Reactivation Risk for clinical purposes. A similar
structure can be employed to study infectious agent clearance and
or immunity to it.
Example 24
Monitoring for Allergic Response During Immunotherapy
Allergic rhinitis is a common condition afflicting .about.11% of
the US population. This is typically an allergy to pollen or dust.
Eliminating the exposure is difficult and it involves vigilant
effort. The most common treatments used in chronic rhinitis are
decongestants, antihistamines, and nasal steroids. In severe cases
immunotherapy is done. The goal of the immunotherapy is to
de-sensitize the patient. First a challenge with many potential
allergens is done to identify the specific allergen the patient is
reacting to. Then the patient is injected with increasing amount of
allergen over a period of months to years until a maintenance dose
is achieved, and the treatment is then continued for several years.
Typically the patient can feel an improvement in symptoms within
3-6 months, but that can also be as late as 12-18 months, but a
large fraction of the patients do not benefit from the treatment or
have relapses. One reason for the slow dose escalation is the risk
of anaphylaxis if the patient is given a high dose of allergen
before s/he sufficiently de-sensitized.
In one embodiment of this invention TCR (and/or BCR) profiles are
used to assess the state of disease in allergic rhinitis and
generate an Allergy Score that predicts how prone the patient to
mount an allergic response should s/he be exposed to the relevant
allergen. It is conceived that a discovery study can be performed
to determine the likelihood of allergy response given the profile
of blood TCR (and/or BCR). This can be used in tailoring the
immunotherapy treatment. Possible clinical decision can be to
discontinue the treatment if it is deemed ineffective, continue the
injection regimen, or accelerate the treatment to reach the
maintenance dose faster.
Discovery of Correlating Clonotypes Using a Population Study
In this embodiment of the invention a population of allergic
rhinitis patients on immunotherapy with blood samples with known
clinical outcome can be used. TCR (and/or BCR) from all these
samples can be sequenced and correlation of individual clonotypes
with allergy outcome can be used to distinguish correlating from
non-correlating clonotypes. Subsequently, parameters can be derived
that distinguish those two classes of clonotypes. These parameters
can include 1) Sequence motif: The motif can be a specific V or J
region, a combination VJ, or short sequences in DJ region that is
associated with a clonotype being correlating; 2) Size of the
clonotype; 3) Level: Absolute level (number of reads per million)
or rank level; 4) Similarity to other clonotypes: the presence of
other highly related clonotypes, like those with silent changes
(nucleotide differences that code for same amino acids) or those
with conservative amino acid changes; 5) For the BCRs the level of
somatic mutations in the clonotype and/or the number of distinct
clonotypes that differ by somatic mutations from some germline
clonotype. 6) Presence in a cell carrying a specific marker. An
alternative or supplemental method to define the correlating and
non-correlating clonotype would use biopsy of positive allergy test
material from patients positive for a specific allergen. At the
site of injection of the allergen it is expected that there will be
great enrichment of the correlating clonotypes. Parameters to
distinguish these from the other clonotypes can be identified as
discussed previously.
The profile data from the blood samples is then used to predict the
allergy state. Given the known outcomes in this training study one
can devise, a model using the standard cross validation techniques
that generates an Allergy Score given the level of the different
clonotypes. Given the profile in a new blood sample of TCR (and/or
BCR) at a specific point, an Allergy Score can be generated to
estimate the degree to which this patient is prone to mount an
allergic response.
Discovery of Correlating Clonotypes Using a Calibration Test
In another embodiment a method of identifying correlating
clonotypes can be implemented using a calibration test for each
patient. This method involves a biopsy sample from a site with a
positive allergen response be taken from the patient. This can be
from the initial allergy test that was performed to determine the
specific allergen the patient is responding to or sample from the
site of any further treatment injections. This can be done more
than once to ensure that the appropriate clonotypes are being
followed in case there is some epitope spreading. TCR and/or BCR
from these biopsy samples can be used to identify the correlating
clonotypes as defined by those that are prevalent in this sample.
This set of clonotypes can then be followed in blood and a score is
generated for the likelihood of allergy response. The algorithm to
generate the Allergy Score is derived through a discovery study
that is similar to the one described above that utilizes the
available clinical data and the levels of the correlating
clonotypes to generate an Allergy Score that estimates the allergy
state.
Discovery of Correlating Clonotypes Using a Calibration Test and a
Population Study
In another embodiment, the identification of the correlating
clonotypes can be achieved through a combination of the above
approaches. Specifically this can be achieved by using the
population study to generate an algorithm to predict correlating
clonotypes. In addition it can be achieved through calibration data
from the same patient using biopsy from a site with a positive
allergen response. A more preferred embodiment will employ both
approaches: population-built algorithm and individual calibration
to most accurately identify the correlating clonotypes. An Allergy
Score is then generated using the level of these clonotypes to
predict the state of allergy through the use of the population
study as a training set.
While preferred embodiments of the present invention have been
shown and described herein, it will be obvious to those skilled in
the art that such embodiments are provided by way of example only.
Numerous variations, changes, and substitutions will now occur to
those skilled in the art without departing from the invention. It
should be understood that various alternatives to the embodiments
of the invention described herein may be employed in practicing the
invention. It is intended that the following claims define the
scope of the invention and that methods and structures within the
scope of these claims and their equivalents be covered thereby.
SEQUENCE LISTINGS
1
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72gtgcgacagg cccccggaca a 217321DNAArtificial SequenceDescription
of Artificial Sequence Synthetic primer 73gtgcgacagg cccccagaca a
217421DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 74tccgccagcc cccagggaag g 217521DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
75tccggcagcc cccagggaag g 217621DNAArtificial SequenceDescription
of Artificial Sequence Synthetic primer 76tccggcagcc accagggaag g
217721DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 77tccgccagca cccagggaag g 217819DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
78tccggcagcc cgccgggaa 197919DNAArtificial SequenceDescription of
Artificial Sequence Synthetic primer 79tccggcagcc gccggggaa
198021DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 80tccggcagcc cgctgggaag g 218121DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
81tccgccagcc cctagggaag g 218221DNAArtificial SequenceDescription
of Artificial Sequence Synthetic primer 82ggtccgccag gctccaggga a
218321DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 83gttccgccag gctccaggga a 218421DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
84ggtccgccag gcttccggga a 218521DNAArtificial SequenceDescription
of Artificial Sequence Synthetic primer 85ggtccgtcaa gctccgggga a
218621DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 86gatccgccag gctccaggga a 218721DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
87ggtccgccaa gctccaggga a 218821DNAArtificial SequenceDescription
of Artificial Sequence Synthetic primer 88ggtccgccag gctccaggca a
218921DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 89ggtccgccag gccccaggca a 219021DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
90ggtccgccag gctccgggca a 219124DNAArtificial SequenceDescription
of Artificial Sequence Synthetic primer 91gggtccgtca agctccaggg
aagg 249224DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 92ctgggtccgc caagctacag gaaa 249321DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
93ggtccgccag cctccaggga a 219421DNAArtificial SequenceDescription
of Artificial Sequence Synthetic primer 94ggtccggcaa gctccaggga a
219525DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 95ctaaaggctg aggacactgc cgtgt 259625DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
96ctctgtgact cccgaggaca cggct 259722DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
97agtggagcag cctgaaggcc tc 229825DNAArtificial SequenceDescription
of Artificial Sequence Synthetic primer 98tgaccaacat ggaccctgtg
gacac 259925DNAArtificial SequenceDescription of Artificial
Sequence Synthetic primer 99acatggagct gagcagcctg agatc
2510025DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 100acatggagct gagcaggctg agatc
2510125DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 101acatggagct gaggagcctg agatc
2510228DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 102acatggagct gaggagccta agatctga
2810322DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 103gagctctgtg accgccgcgg ac 2210423DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
104gagctctgtg accgccgtgg aca 2310525DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
105gagctctgtg accgctgcag acacg 2510623DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
106gagctctgtg accgctgcgg aca 2310725DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
107gagctctgtg actgccgcag acacg 2510825DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
108gagctctgtg actgcagcag acacg 2510923DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
109gagctctgtg actgccgcgg aca 2311022DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
110gagctctgtg accgcggacg cg 2211121DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
111ggctctgtga ccgccgcgga c 2111223DNAArtificial SequenceDescription
of Artificial Sequence Synthetic primer 112gagctctgtg accgccgcag
aca 2311323DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 113gagctctgtg accgctgaca cgg 2311428DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
114caaatgaaca gcctgagagc cgaggaca
2811528DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 115caaatgaaca gcctgaaaac cgaggaca
2811628DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 116caaatgaaca gtctgaaaac cgaggaca
2811728DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 117caaatgatca gcctgaaaac cgaggaca
2811830DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 118caaatgaaca gtctgagaac tgaggacacc
3011928DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 119caaatgaaca gtctgagagc cgaggaca
2812028DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 120caaatgaaca gcctgagagc tgaggaca
2812128DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 121caaatgagca gcctgagagc tgaggaca
2812228DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 122caaatgaaca gcctgagaga cgaggaca
2812328DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 123caaatgggca gcctgagagc tgaggaca
2812426DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 124caaatgaaca gcctgagagc cgggga
2612528DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 125caaatgaaca gtctgagagc tgaggaca
2812628DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 126caaatgagca gtctgagagc tgaggaca
2812720DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 127gccaggggga agaccgatgg 2012820DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
128gccaggggga agacggatgg 2012950DNAArtificial SequenceDescription
of Artificial Sequence Synthetic primer 129aatgatacgg cgaccaccga
gatctgggaa gacgatgggc ccttggtgga 5013031DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
130aggacctgaa aaacgtgttc ccacccgagg t 3113131DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
131aggacctgaa caaggtgttc ccacccgagg t 3113249DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
132cctccaccaa gggcccatcg gtcttccccc tggcgccctg ctccaggag
4913349DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 133cttccaccaa gggcccatcc gtcttccccc tggcgccctg
ctccaggag 4913449DNAArtificial SequenceDescription of Artificial
Sequence Synthetic primer 134cttccaccaa gggcccatcg gtcttccccc
tggcgccctg ctccaggag 4913520DNAArtificial SequenceDescription of
Artificial Sequence Synthetic primer 135agcgacctcg ggtgggaaca
20
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References